Symbol	Variation type	refSNP ID	Detected method	Disease	Risk type	Result	Mechanism	PMID	Details
HLA-DRB1	genotype	DR2	PCR	MS	Disease risk	We found significant associations with HLA-Cw3 (p -- 0.002, Pc = 0.012, RR = 3.2), DR2 (p = 0.007, RR = 2.6), and DQBI*0602 (p = 0.04, RR = 4.0) in Japanese patients for the first time.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DRB1	polymorphisms	DRB1*11	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
NFKBIA	SNP	rs2233408	PCR	MS	Disease risk	The differences of genotype frequencies of IKBa -519 C/T between the patients with multiple sclerosis and the controls were not significant.	NF-kB plays a substantial role in inflammatory diseases and in the development of autoimmunity such as multiple sclerosis .The anti-apoptogenic effect of NF-jB is well documented. Inhibitor of kappa B (IkB) is an inhibitor of NF-kB, which binds withNF-kB in the cytoplasm and controls the transcriptional activity of NF-kB.	24368589	Details
CNTF	mutation	N/A	PCR	MS	Phenotypic risk	The frequency of patients with early or late onset of the disease and clinical course of RRMS, SPMS or PPMS was not different in patients homozygous for the CNTF 01 allele or those heterozygous for the CNTF alleles 01 and 02.The CNTF-genotype was not correlated with disease progression, ie, similar frequencies were obtained for patients classified as having less severe, moderately severe or severe MS.	While CNTF was initially characterized as a trophic factor for neurons5–7 more recent evidence supports the role for survival, proliferation, and maturation of oligodendrocyte lineage cells.In addition CNTF protects oligodendrocytes from TNF-α induced cell death and was found to be increased in cerebrospinal fluid (CSF) of MS patients recovering from acute exacerbations.	11857064	Details
PRF1	mutations	N/A	PCR	MS	Disease risk	A91V and possibly other perforin variations indicate susceptibility to MS.	mutations	18496551	Details
HLA-DRB1	Allele	NA	PCR	MS	Disease risk	We confirmed that HLA-DRB1*15:01 showed the strongest association with MS	In auto-immune diseases, such as rheumatoid arthritis, psoriasis, and type 1 diabetes, fine-mapping studies have identified strong genetic risk variants in the MHC region	31382992	Details
IL2RA	SNP	rs2104286	PCR	MS	Disease risk	The gene polymorphisms at the loci of IL2RA rs2104286 and rs12722489 are closely associated with susceptibility to MS in the Han and Hui nationalities.	Thus,the correlation between IL2RA SNPs and MS susceptibility may be related to its involvement in immune regulation, and more researches are urgent to study the underlying mechanisms.	30352019	Details
HLA-DRB1	genotype	DR4	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DRB1	polymorphisms	DRB1*13	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
HLA-B	Allele	NA	PCR	MS	Disease risk	Stepwise conditional analysis identified HLA-DRB1*04:05,	In auto-immune diseases, such as rheumatoid arthritis, psoriasis, and type 1 diabetes, fine-mapping studies have identified strong genetic risk variants in the MHC region	31382992	Details
IL2RA	SNP	rs12722489	PCR	MS	Disease risk	The gene polymorphisms at the loci of IL2RA rs2104286 and rs12722489 are closely associated with susceptibility to MS in the Han and Hui nationalities.	Thus,the correlation between IL2RA SNPs and MS susceptibility may be related to its involvement in immune regulation, and more researches are urgent to study the underlying mechanisms.	30352019	Details
NCF1	marker	D7S1870	PCR	MS	Disease risk	This analysis showed suggestive association signals for NCF1 and CYBB (lowest p = 0.038 and p = 0.013, respectively).	N/A	30567305	Details
HLA-DRB1	genotype	DR5	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DRB1	polymorphisms	DRB1*14	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
HLA-DRB1	amino acid polymorphisms	NA	PCR	MS	Disease risk	HLA-B*39:01, and HLA-B*15:01 as being associated with independent MS susceptibility	In auto-immune diseases, such as rheumatoid arthritis, psoriasis, and type 1 diabetes, fine-mapping studies have identified strong genetic risk variants in the MHC region	31382992	Details
CXCR5	SNP	rs3922	PCR	MS	N/A	In this study, our findings showed that the occurrence and development of MS had no significant relationship with CXCR5 rs3922.	Therefore, we speculate thatCXCR5 SNPs may affect its expression, thereby influencing the immune signals it participates in and thus affecting the occurrence and development of MS.	30352019	Details
NCF1	marker	D7S2518	PCR	MS	Disease risk	This analysis showed suggestive association signals for NCF1 and CYBB (lowest p = 0.038 and p = 0.013, respectively).	N/A	30567305	Details
HLA-DRB1	genotype	DR6	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DRB1	polymorphisms	DRB1*1501	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
HLA-DRB1	SNP	rs703842	PCR	MS	Disease risk	For the first time in Central European Slovak population, we found the rs703842 allele C to be protective factor against MS development	In addition, the study of Simon et al. (2011) showed that the association of rs703842 with MS risk could be dependent on the pre-sence of Human Leucocyte Antigen (HLA) DRB1*15:01 allele, that is known to be one of the most important genetic MS susceptibility factors	30875612	Details
NCF2	SNP	rs796860	PCR	MS	Disease risk	This analysis showed suggestive association signals for NCF1 and CYBB (lowest p = 0.038 and p = 0.013, respectively).	N/A	30567305	Details
HLA-DRB1	genotype	DR7	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DRB1	polymorphisms	DRB1*16	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
TGFB1	Allele	NA	PCR	MS	Disease risk	Transforming growth factor b1 TGFb1 is a Th2 cytokine encoded on chromosome 19q13, a region possibly linked to multiple .sclerosis MS . TGFb1 exerts favorable effects on experimental allergic encephalomyelitis.	Transforming growth factor beta1 (TGFbeta1) is a Th2 cytokine encoded on chromosome 19q13, a region possibly linked to multiple sclerosis (MS).	11694328	Details
NCF2	SNP	rs2296164	PCR	MS	Disease risk	This analysis showed suggestive association signals for NCF1 and CYBB (lowest p = 0.038 and p = 0.013, respectively).	N/A	30567305	Details
HLA-DRB1	genotype	DR8	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DQB1	polymorphisms	DQB1*0201	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
TNF	polymorphisms	Chr 6p21	PCR	MS	Disease risk	Two microsatellite markers were significant: D3S1278 (Chr 3q13, P < 0.001) and tumor necrosis factor (TNF)-α (Chr 6p21, P < 0.001).	N/A	19244395	Details
IL7R	SNP	NA	PCR	MS	Disease risk	There were trends towards an increase of the GTG+ haplotype (odds ratio 1.45), and under-representation of the TTA+ haplotype (OR 0.65) in DRB1*1501-positive MS cases, suggesting that larger sample sizes and comparison in more defined MS patient groups may support an association with the IL-7R gene.	We have investigated the interleukin-7 receptor (IL-7R) a-chain gene as a positional and functional candidate gene for susceptibility to multiple sclerosis (MS), in view of its chromosomal location on 5p14–p12, a region that has shown suggestive linkage in MS genome screens, and its role in T- and B-cell proliferation and reactivity.	12825072	Details
NCF2	SNP	rs3818364	PCR	MS	Disease risk	This analysis showed suggestive association signals for NCF1 and CYBB (lowest p = 0.038 and p = 0.013, respectively).	N/A	30567305	Details
HLA-DRB1	genotype	DR9	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DQB1	polymorphisms	DQB1*0202	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
TNF	polymorphisms	Chr 3q13	PCR	MS	Disease risk	Two microsatellite markers were significant: D3S1278 (Chr 3q13, P < 0.001) and tumor necrosis factor (TNF)-α (Chr 6p21, P < 0.001).	N/A	19244395	Details
TNF	allele	TNFa allele,TNFb allele,TNFa, b combination	PCR	MS	Disease risk	None of these microsatellite combinations or any others showed any association with disease.	N/A	10626741	Details
HLA-DQA1	Allele	NA	PCR	MS	Disease risk	Similar results have been described in other Caucasian populations living in non tropical areas. Before results could indicate that the Caucasoid populations genetic component implied in the susceptibility to MS have remained in Paisa community, whether the environmental component, being meaningful to develop MS.	Discrimination and quantification of the environmental and genetic components involved in developing multiple sclerosis (MS) have not been made. In order to discriminate these components we have ascertained affected individuals by MS belonging to the Paisa community from Antioquia, Colombia, a state localized in the tropical area of South America, to detect eventual linkage disequilibrium to HLA, locus DQ alpha, which could demonstrate the relevance of the genetic component.	10730325	Details
NCF2	SNP	rs789192	PCR	MS	Disease risk	This analysis showed suggestive association signals for NCF1 and CYBB (lowest p = 0.038 and p = 0.013, respectively).	N/A	30567305	Details
HLA-DRB1	genotype	DR10	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DQB1	polymorphisms	DQB1*0301	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
TNF	polymorphisms	Chr 2q14	PCR	MS	Phenotypic risk	A further three markers were significant in our preliminary analysis suggesting a trend toward impact on disease outcome; D4S432 (Chr 4p16, P = 0.001), D2S347 (Chr 2q14, P = 0.003), and D19S903 (Chr 19p13, P = 0.003).	N/A	19244395	Details
DBP	SNP	rs7041, rs4588	PCR	MS	Disease risk	No association was found in blacks regardless of genotype.	N/A	29414925	Details
IGH	Allele	NA	PCR	MS	Disease risk	We conclude that the IgH chain genes are unlikely to playa role in genetic susceptibility to MS in the Swedish population.	Multiple sclerosis (MS) is a demyelinating inflammatory disease of the central nervous system. Autoantibodies are thought to participate in the pathogenesis. Previous reports on the role of immunoglobulin (Ig) variable gene segments in MS are contradictory.	9306094	Details
NCF2	SNP	rs2274065	PCR	MS	Disease risk	This analysis showed suggestive association signals for NCF1 and CYBB (lowest p = 0.038 and p = 0.013, respectively).	N/A	30567305	Details
HLA-DRB1	genotype	DRw52	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DQB1	polymorphisms	DQB1*0302	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
TNF	polymorphisms	Chr 19p13	PCR	MS	Phenotypic risk	A further three markers were significant in our preliminary analysis suggesting a trend toward impact on disease outcome; D4S432 (Chr 4p16, P = 0.001), D2S347 (Chr 2q14, P = 0.003), and D19S903 (Chr 19p13, P = 0.003).	N/A	19244395	Details
MTHFR	missense	C677T	PCR	MS	Disease risk	No significant differences were found in the frequency of the MTHFR C677T polymorphism between MS patients and healthy controls.	Methylenetetrahydrofolate reductase (MTHFR) is a folate dependent enzyme which regulates a key metabolic intersection in the folate pathway.	23523621	Details
DBP	SNP	rs7041, rs4588	PCR	MS	Disease risk	No association was found in Hispanics regardless of genotype.	N/A	29414925	Details
APOE	gene polymorphism	-491 A/T	PCR	MS	Disease risk	The AA homozygous state of the -491 AIT polymorphism of the APOE regulatory region is associated with I cognitive impairment in patients with MS.	gene polymorphism	10536914	Details
CCR5	SNP	rs333	PCR	MS	Disease risk	Our results indicate no association between the CCR5 D32 allele and MS.	The roles of chemokine receptor V (CCR5) and its polymorphism, rs333 in multiple sclerosis (MS) are controversial.	25500253	Details
NCF4	SNP	rs1883112	PCR	MS	Disease risk	This analysis showed suggestive association signals for NCF1 and CYBB (lowest p = 0.038 and p = 0.013, respectively).	N/A	30567305	Details
HLA-DRB1	genotype	DRw53	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DQB1	polymorphisms	DQB1*0303	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
TNF	polymorphisms	Chr 4p16	PCR	MS	Phenotypic risk	A further three markers were significant in our preliminary analysis suggesting a trend toward impact on disease outcome; D4S432 (Chr 4p16, P = 0.001), D2S347 (Chr 2q14, P = 0.003), and D19S903 (Chr 19p13, P = 0.003).	N/A	19244395	Details
MTHFR	missense	A1298C	PCR	MS	Disease risk	However, the genotype prevalence of the missense variant MTHFR A1298C was significantly different between patients and controls.	Methylenetetrahydrofolate reductase (MTHFR) is a folate dependent enzyme which regulates a key metabolic intersection in the folate pathway.	23523621	Details
DBP	SNP	rs7041, rs4588	PCR	MS	Disease risk	In models stratified by race/ethnicity, higher serum 25OHD levels were strongly associated with a lower risk of MS/CIS in whites who carried at least one copy of the C allele at rs7041 but not in those homozygous for the A allele.	N/A	29414925	Details
IL4	VNTR (variable number tandem repeat)	3 VNTR (variable number tandem repeat)	PCR	MS	Disease risk	The results of this study suggest that intron 3 VNTR polymorphism of the IL-4 gene was pos-itively associated with predisposition to develop MS in Turkish population.	Genetic risk factors are known to contribute to the etiology of multiple sclerosis (MS). Interleu-kin (IL)-4 gene polymorphisms have been associated with immune-mediated diseases. The aim of this study was to explore the frequency of IL-4 gene intron 3 VNTR (variable number tandem repeat) poly-morphism in a cohort of Turkish patients with MS.	23756167	Details
NCF4	SNP	rs741999	PCR	MS	Disease risk	This analysis showed suggestive association signals for NCF1 and CYBB (lowest p = 0.038 and p = 0.013, respectively).	N/A	30567305	Details
HLA-DRB1	polymorphisms	DRB1*1501	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DQB1	polymorphisms	DQB1*0402	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
SPP1	polymorphisms	5891C/T	PCR	MS	Phenotypic risk	Interestingly, individuals carrying the 5891C allele, which is more prevalent in patients with MS in Japanese populations, displayed significantly lower levels of total serum IgE.	the SPP1 gene may represent a genetic factor that plays a role in basal IgE production in a nonantigen-specific (non-cognate) fashion.	16433860	Details
APOE	Allele	NA	PCR	MS	Phenotypic risk	An association with the o4 allele was evident in this study, but only in cases of severe cognitive impairment.	N/A	17294608	Details
CYBA	SNP	rs4673	PCR	MS	Disease risk	This analysis showed suggestive association signals for NCF1 and CYBB (lowest p = 0.038 and p = 0.013, respectively).	N/A	30567305	Details
HLA-DRB1	polymorphisms	DRB1*1502	PCR	MS	Disease risk	Frequencies of HLA-DR in 44 MS patients and 140 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DQB1	polymorphisms	DQB1*0501	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
SPP1	polymorphisms	7052T/C	PCR	MS	Phenotypic risk	Associations between these SPP1 polymorphisms and total serum Ig E levels remained significant even after adjusting for the presence of atopy (P = 0.012 for 5891 C/T; P = 0.002 for 7052 T/C).	the SPP1 gene may represent a genetic factor that plays a role in basal IgE production in a nonantigen-specific (non-cognate) fashion.	16433860	Details
VDR	intragenic restriction fragment length polymorphisms	N/A	PCR	MS	Disease risk	Our results support a role for the VDR gene increasing the risk of developing multiple sclerosis, particularly the progressive clinical subtypes of MS.	The Taq and Apa variants are in very strong and significant linkage disequilibrium (D0 0.96, P < 0.0001). The genotypic associations are strongest for the progressive forms of MS (SP–MS and PP–MS)	16076630	Details
LILRA3	deletion	N/A	PCR	MS	Disease risk	We analyse here two series of Spanish patients and healthy controls and show that relapsing MS (R-MS) is associated with a gene deletion affecting the hypothetically soluble leukocyte immunoglobulin (Ig)-like receptor A3 (LILRA3, 19q13.4), in agreement with an earlier finding in German patients.	N/A	19421224	Details
CYBA	SNP	rs2306422	PCR	MS	Disease risk	This analysis showed suggestive association signals for NCF1 and CYBB (lowest p = 0.038 and p = 0.013, respectively).	N/A	30567305	Details
HLA-DRB1	polymorphisms	DRB1*1601	PCR	MS	Disease risk	Frequencies of HLA-DR in 44 MS patients and 140 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DQB1	polymorphisms	DQB1*0502	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
SPP1	polymorphisms	1687A/G	PCR	MS	Phenotypic risk	The 1687A/G, 381T/C and 94 deletion/G polymorphisms displayed no association with total serum IgE levels.	the SPP1 gene may represent a genetic factor that plays a role in basal IgE production in a nonantigen-specific (non-cognate) fashion.	16433860	Details
ENPEP	intragenic restriction fragment length polymorphisms	N/A	PCR	MS	Disease risk	Our results support a role for the VDR gene increasing the risk of developing multiple sclerosis, particularly the progressive clinical subtypes of MS.	The Taq and Apa variants are in very strong and significant linkage disequilibrium (D0 0.96, P < 0.0001). The genotypic associations are strongest for the progressive forms of MS (SP–MS and PP–MS)	16076630	Details
CYBB	SNP	rs5963310	PCR	MS	Disease risk	This analysis showed suggestive association signals for NCF1 and CYBB (lowest p = 0.038 and p = 0.013, respectively).	N/A	30567305	Details
HLA-DRB1	polymorphisms	DRB1*1602	PCR	MS	Disease risk	Frequencies of HLA-DR in 44 MS patients and 140 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DQB1	polymorphisms	DQB1*0503	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
SPP1	polymorphisms	381T/C	PCR	MS	Phenotypic risk	The 1687A/G, 381T/C and 94 deletion/G polymorphisms displayed no association with total serum IgE levels.	the SPP1 gene may represent a genetic factor that plays a role in basal IgE production in a nonantigen-specific (non-cognate) fashion.	16433860	Details
CD24	SNP	CD24V/V	PCR	MS	Disease risk	Our data revealed that the susceptibility and the progression of MS in individuals with the CD24V/V genotype were greater than in those with the CD24A/V and CD24A/A genotypes	The CD24 protein，which is expressed by a variety of cells,is involved in the immune system	19896210	Details
HLA-DRB1	HLA-DRB1(*)0406	N/A	PCR	MS	Disease risk	Southern Han MS patients may be linked to the HLA-DRB1(*)0406, DRB1(*)1302, DRB1(*)120201 and DPB1(*)2101, but not to the HLA-DRB1(*)1501 or DPB1(*)0501 alleles as reported in the above populations.	N/A	18167262	Details
CYBB	SNP	rs9330580	PCR	MS	Disease risk	This analysis showed suggestive association signals for NCF1 and CYBB (lowest p = 0.038 and p = 0.013, respectively).	N/A	30567305	Details
HLA-DRB1	polymorphisms	DQB1*0501	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DQB1	polymorphisms	DQB1*0601	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
SPP1	polymorphisms	94 deletion/G	PCR	MS	Phenotypic risk	The 1687A/G, 381T/C and 94 deletion/G polymorphisms displayed no association with total serum IgE levels.	the SPP1 gene may represent a genetic factor that plays a role in basal IgE production in a nonantigen-specific (non-cognate) fashion.	16433860	Details
CD24	SNP	CD24A/V	PCR	MS	Disease risk	Our data revealed that the susceptibility and the progression of MS in individuals with the CD24V/V genotype were greater than in those with the CD24A/V and CD24A/A genotypes	The CD24 protein，which is expressed by a variety of cells,is involved in the immune system	19896210	Details
HLA-DQA1	Allele	NA	PCR	MS	Disease risk	The correlation of the HLA-DQA1*04:01 allele with a higher lesion load on T2/Flair MRI sequences suggests that the presence of this allele is associated with the risk of greater MS severity.	The genetic predisposition to multiple sclerosis (MS) is associated with HLA alleles, especially HLA-DRB1*15:01.	34877984	Details
HLA-DRB1	DRB1(*)1302, DRB1(*)120201 and DPB1(*)2101	N/A	PCR	MS	Disease risk	Southern Han MS patients may be linked to the HLA-DRB1(*)0406, DRB1(*)1302, DRB1(*)120201 and DPB1(*)2101, but not to the HLA-DRB1(*)1501 or DPB1(*)0501 alleles as reported in the above populations.	N/A	18167262	Details
HLA-DRB1	polymorphisms	DQB1*0502	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DQB1	polymorphisms	DQB1*0602	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
HLA-DRB1	polymorphisms	DRB1*0101	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
CD24	SNP	CD24A/A	PCR	MS	Disease risk	Our data revealed that the susceptibility and the progression of MS in individuals with the CD24V/V genotype were greater than in those with the CD24A/V and CD24A/A genotypes	The CD24 protein，which is expressed by a variety of cells,is involved in the immune system	19896210	Details
CTLA4	Allele	NA	PCR	MS	Phenotypic risk	This CTLA-4 polymorphism may modulate the prognosis of patients with MS and may be relevant to generation of OCB in the CSF.	Multiple sclerosis (MS) is widely believed to have a T-cell-mediated autoimmune etiology. The CTLA-4 gene is a strong candidate for involvement in autoimmune diseases because it plays an important role in the termination of T-cell activation.	10567049	Details
HLA-DRB1	DRB1(*)120201 and DPB1(*)2101	N/A	PCR	MS	Disease risk	Southern Han MS patients may be linked to the HLA-DRB1(*)0406, DRB1(*)1302, DRB1(*)120201 and DPB1(*)2101, but not to the HLA-DRB1(*)1501 or DPB1(*)0501 alleles as reported in the above populations.	N/A	18167262	Details
HLA-DQB1	polymorphisms	DQB1*0503	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DQB1	polymorphisms	DQB1*0603	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
HLA-DRB1	polymorphisms	DRB1*0102	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
ACE	SNP	DD genotype	PCR	MS	Disease risk	DD genotype of ACE gene might contribute to a higher risk of developing MS in men	the blockade of ACE suppresses the disease itself	17083336	Details
APOE	Allele	NA	PCR	MS	Phenotypic risk	Apo E genotypes do not influence the development of MS and ON. The Apo o4 allele seems to predispose carriers with MS to a faster progression of diseas	T o investigate the association between apolipoprotein E (Apo E) genotype in multiple sclerosis (MS) and acute monosymptomatic optic neuritis (ON) in a genetically homogeneous population with a high frequency of the Apoo4 allele.	16193886	Details
HLA-DRB1	DPB1(*)2101	N/A	PCR	MS	Disease risk	Southern Han MS patients may be linked to the HLA-DRB1(*)0406, DRB1(*)1302, DRB1(*)120201 and DPB1(*)2101, but not to the HLA-DRB1(*)1501 or DPB1(*)0501 alleles as reported in the above populations.	N/A	18167262	Details
IL25	polymorphisms	IL-25 exon1	PCR	MS	Disease risk	However, no significant differences were found in polymorphisms for IL-25 exon.	Considering the role of IL-25 in suppression of the effects of IL-17A and active phase of Experimental Autoimmune Encephalomyelitis (EAE) in vivo	25143869	Details
HLA-DQB1	polymorphisms	DQB1*0601	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DQB1	polymorphisms	DQB1*0604	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
HLA-DRB1	polymorphisms	DRB1*0103	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
IL4	gene polymorphisms	C/C, T/C, and T/T genotypes of the -590 region of IL-4	PCR	MS	Disease risk	We observed a significant difference in the C/C, T/C, and T/T genotypes of the -590 region of IL-4 between patients with MS and healthy controls (P<.001).	We conclude that functional polymorphisms of IL-4 possibly play a crucial role in the pathogenesis of MS.	22366824	Details
STMN1	SNP	rs182455	PCR	MS	Disease risk	the rs182455 polymorphism does not influence MS susceptibility or clinical disease course	We conclude that despite potential importance of stathmin in the pathogenesis of MS	19012073	Details
CTLA4	Allele	NA	PCR	MS	Disease risk	Our results suggest that CTLA-4 gene polymorphisms are neither conclusively related to susceptibility nor to the clinical characteristics of MS, especially in Japanese patients with conventional/classical form and clinical features identical to those of their counterparts in Western countries.	We investigated the polymorphisms of exon 1 (+49A/G) and promoter (?318C/T and ?651C/T) regions of the CTLA-4 gene in 133 Japanese patients with conventional/classical multiple sclerosis (MS) and 156 healthy controls. Patients with optico-spinal MS (OSMS) or atypical clinical attacks were excluded from the study. There was no significant difference in the distribution of polymorphisms between patients and controls.	15652423	Details
IL25	polymorphisms	IL-25 exon2	PCR	MS	Disease risk	However, no significant differences were found in polymorphisms for IL-25 exon.	Considering the role of IL-25 in suppression of the effects of IL-17A and active phase of Experimental Autoimmune Encephalomyelitis (EAE) in vivo	25143869	Details
HLA-DRB1	polymorphisms	DQB1*0602	PCR	MS	Disease risk	We found significant associations with HLA-Cw3 (p -- 0.002, Pc = 0.012, RR = 3.2), DR2 (p = 0.007, RR = 2.6), and DQBI*0602 (p = 0.04, RR = 4.0) in Japanese patients for the first time.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DQA1	polymorphisms	DQA1*0101	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
HLA-DRB1	polymorphisms	DRB1*1501	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
HLA-DRB1	allele	N/A	PCR	MS	Phenotypic risk	HLA DRB1*15 allele was related with an earlier manifestation of the first MS symptoms, progressive course of the disease and higher degree of disability. HLA DRB1*08 allele was more prevalent among the RR MS patients and was associated with the lower rate of relapse, degree of disability and IgG index.	N/A	23837503	Details
ACE	insertion/deletion gene polymorphism	N/A	PCR	MS	Disease risk	The ACE I/D polymorphism and pretreatment relapse rate accounted for ～26.7% of the IFN-β response variability among the men in the sample	the negative response to IFN-尾 therapy was associated with the ACE-DD genotype in men	28430710	Details
PTPRC	SNP	NA	PCR	MS	Disease risk	We conclude that the 77C0/G PTPRC polymorphism is present and preferentially transmitted in a small subgroup (B/5%) of MS families,which may only be detected with complementary methods of analysis	The 77C0/G polymorphism in exon 4 of CD45 or protein tyrosine phosphatase receptor-type C (PTPRC) has been investigated in families with multiple sclerosis (MS) and in several cohorts of sporadic patients and controls, however, with conflicting results.	15584483	Details
CD24	Ala/Val	N/A	PCR	MS	N/A	In conclusion, we were unable to confirm previous findings by Zhou et al. (2003) of a positive association between the CD24v/v genotype and susceptibility to or progression of MS in our study population of over 300 Belgian and over 800 UK cases and controls.	N/A	16631259	Details
HLA-DQB1	polymorphisms	DQB1*0603	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DQA1	polymorphisms	DQA1*0102	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
HLA-DRB1	polymorphisms	DRB1*1502	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
HLA-DPB1	allele	DRB1*1501	PCR	MS	Disease risk	DRB1*1501 was not associated with DPB1*0301 nor DPB1*0501 in either patients or controls (data not shown), and the linkage disequilibria between these alleles were also not found in a large Japanese population	N/A	10777094	Details
HLA-DRB1	amino acid polymorphisms	NA	PCR	MS	Disease risk	There were no significant associations between the presence of HLA DRB1*1501 allele and the clinical symptoms, course of disease, or disability score.	A great vari-ety of recently reported linkage and genome-wide association studies have established that the most important genetic risk factor in MS is carriage of a single copy of the HLA class II allele DRB1*15 to homozygote forms (6–8). About 60% of MS patients in Northern Europe are positive for HLA-DRB1*15, compared with 30% of healthy controls	22112985	Details
SLC11A1	5'GT repeat	N/A	PCR	MS	N/A	We found no evidence of association between SLC11A1 polymorphisms and MS susceptibility in the Spanish population.	N/A	15584484	Details
HLA-DQB1	polymorphisms	DQB1*0604	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DQA1	polymorphisms	DQA1*0103	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
HLA-DRB1	polymorphisms	DRB1*1601	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
CLEC16A	SNP	rs725613, rs2041670, rs2080272, rs998592	PCR	MS	Disease risk	Four SNPs located in intron 19 of the CLEC16A gene were found associated.	N/A	20849399	Details
HLA-DPB1	allele	DPB1*0301	PCR	MS	Disease risk	DRB1*1501 was not associated with DPB1*0301 nor DPB1*0501 in either patients or controls (data not shown), and the linkage disequilibria between these alleles were also not found in a large Japanese population	N/A	10777094	Details
CTLA4	Allele	NA	PCR	MS	Disease risk	In spite of some previous reports, this study did not confirm any significant association with alleles and genotypes of SNPs of the CTLA4 in Iranian MS patients. Such disparity could be due to genetic background, ethnicity and different forms of the disease.	Multiple sclerosis (MS) is a disease of the central nervous system (CNS) characterized by multiple regions of demyelination and inflammation along axons with a T cell-mediated autoimmune etiology.	21131701	Details
SLC11A1	D543N	N/A	PCR	MS	N/A	We found no evidence of association between SLC11A1 polymorphisms and MS susceptibility in the Spanish population.	N/A	15584484	Details
HLA-DRB1	polymorphisms	DQB1*0301	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DRB1	polymorphisms	HLA-DRB115	PCR	MS	Phenotype risk	MS-associated allele HLA-DRB115 had a higher female-to-male ratio versus those lacking it (P 5 0.00023).	N/A	20634196	Details
HLA-DQA1	polymorphisms	DQA1*0104	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
HLA-DRB1	polymorphisms	DRB1*1602	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
HLA-DPB1	allele	DPB1*0501	PCR	MS	Disease risk	DRB1*1501 was not associated with DPB1*0301 nor DPB1*0501 in either patients or controls (data not shown), and the linkage disequilibria between these alleles were also not found in a large Japanese population	N/A	10777094	Details
CNP	Allele	NA	PCR	MS	Disease risk	While the significance of this is unclear, it would appear unlikely that mutations in the expressed regions of the human CPNase gene contribute to genetic susceptibility to MS in the majority of sufferers.	The amino acid sequence of CNPase shows a C-terminal motif characteristic of proteins involved in signal transduction pathways, suggesting a key role in myelin function.	9050359	Details
SLC11A1	1729 + 55del4	N/A	PCR	MS	N/A	We found no evidence of association between SLC11A1 polymorphisms and MS susceptibility in the Spanish population.	N/A	15584484	Details
HLA-DQB1	polymorphisms	DQB1*0302	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-A	polymorphisms	A2	PCR	MS	Phenotype risk	The HLA B7–A2 haplotype was significantly associated with higher T2-LV and T1-LV and a trend toward lower BPF was observed.	N/A	19232441	Details
HLA-DQA1	polymorphisms	DQA1*0201	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
HLA-DRB1	polymorphisms	DRB1*0301	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
LILRA3	Deletion	6.7-kbp	PCR	MS	Disease risk	There were no significant differences between MS patients and controls.	LILRA3 molecule (Leukocyte immunoglobulin–like subfamily A, member 3), belongs to the family of 13 highly homologous receptors–(LILRs).LILR molecules are broadly expressed on myeloid and lymphoid cells and play an important role in modulating innate and adoptive immune responses.	23238213	Details
VDR	SNP	rs7975232	PCR	MS	Disease risk	We did not find an association of either of the two SNPs with either 25(OH)D or 1,25(OH)2D levels.We did not find an association of these polymorphisms with MS.	N/A	19758194	Details
IFNG	allelic	located in the first intron of the interferon-gamma gene	PCR	MS	Phenotypic risk	Our results show a very different allelic distribution when patients with relapses were compared with relapse-free patients.	Interferon-beta is a biological treatment widely used in multiple sclerosis (MS). However, not every patient responds equally well to this therapy	16430971	Details
NRG1	SNP	rs77493513	PCR	MS	Disease risk	The results show that allele C of rs77493513 polymorphism in the NRG1 gene can be a risk factor for MS	Neuregulin 1 (NRG1) is a signaling protein that plays an important role in a variety of biological processes, including potentiate oligodendrocyte differentiation and myelination in the CNS, immune response regulation, and inflammation.	35106689	Details
SLC11A1	1729 + 271del4	N/A	PCR	MS	N/A	We found no evidence of association between SLC11A1 polymorphisms and MS susceptibility in the Spanish population.	N/A	15584484	Details
HLA-DQB1	polymorphisms	DQB1*0303	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-B	polymorphisms	B7	PCR	MS	Phenotype risk	The HLA B7–A2 haplotype was significantly associated with higher T2-LV and T1-LV and a trend toward lower BPF was observed.	N/A	19232441	Details
HLA-DQA1	polymorphisms	DQA1*0301	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
HLA-DRB1	polymorphisms	DRB1*0303	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
HLA-DRB1	allele	HLA-DRB1*1501	PCR	MS	Disease risk	We observed significantly higher frequency of HLA-DRB1*1501 allele in cases than in controls.	N/A	23238213	Details
VDR	SNP	rs731236	PCR	MS	Disease risk	We did not find an association of either of the two SNPs with either 25(OH)D or 1,25(OH)2D levels.We did not find an association of these polymorphisms with MS.	N/A	19758194	Details
HSPA1B	SNP	rs1061581	PCR	MS	Disease risk	the HSP70-2 rs1061581 polymorphism is related to ROS levels	have a role in the different expression ofHSP70-2 under oxidative stimulus	31720998	Details
MIF	Allele	NA	PCR	MS	Disease risk	This study indicates that the MIF –173 CC genotype may cause susceptibility to multiple sclerosis in the white Turkish population and a younger age of disease onset is associated with this polymorphism.	Elevated levels of macrophage migration inhibitory factor (MIF) have been observed in the cerebrospinal fluid of patients with multiple sclerosis.	20233515	Details
APOE	epsilon4	N/A	PCR	MS	Disease risk	Cognitive decline was predominant in men and was associated with disease duration, Kurtzke Expanded Disability Status Scale (EDSS) score, a low level of education, and, interestingly, the epsilon4 allele of the APOE gene.	N/A	15503099	Details
HLA-DRB1	polymorphisms	DQB1*0401	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
ITGA4	polymorphism	A3061G	PCR	MS	Phenotypic risk	None of the genotypes or alleles com binations of the VLA4 variants were associated with suscep tibility to MS disease.	N/A	17609118	Details
HLA-DQA1	polymorphisms	DQA1*0303	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
HLA-DRB1	polymorphisms	DRB1*0401	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
GRIN2A	SNP	rs3859123	PCR	MS	Phenotypic risk	we show associations between GRIN2A SNPs and phenotypic variation in NBV and NWMV in this first exploratory study	genetic association	22851457	Details
HLA-DRB1	Allele	NA	PCR	MS	Disease risk	We found that several HLA-DRB1 and DQB1 alleles were associated with MS.	Several studies have investigated the association of different HLA antigens with multiple sclerosis (MS).	29131543	Details
HLA-DRB1	HLA-DRB1*15	N/A	PCR	MS	N/A	Our findings suggest that the notion that HLA-DRB1*15 is the sole major-histocompatibility-complex determinant of susceptibility in northern-European populations with MS may be incorrect.	It remains possible that the association of MS with HLA-DRB1*15 is due to linkage disequilibrium with a nearby locus and/or to the presence of disease-influencing allele(s) in DRB1*15-negative haplotypes.	11519010	Details
HLA-DQB1	polymorphisms	DQB1*0402	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
ITGA4	polymorphism	A-269C	PCR	MS	Phenotypic risk	None of the genotypes or alleles com binations of the VLA4 variants were associated with suscep tibility to MS disease.	N/A	17609118	Details
HLA-DQA1	polymorphisms	DQA1*0401	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
HLA-DRB1	polymorphisms	DRB1*01	PCR	MS	Disease risk	A comparison of the transmission of HLA-DRB1 alleles in ASP and AUNN families	N/A	19098025	Details
HLA-DRB1	polymorphisms	DRB1*0402	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
APOE	allele	N/A	PCR	MS	Disease risk	Distribution of APOE genotypes did not differ in patients and control subjects.No variation in risk was found in patients carrying allele 3 in a homozygous state or in those having the 2/3 or 2/2 genotype.	The APOE gene, located in the 19q13 region, codes for a major lipid carrier protein (apoE) in the brain. This protein, associated with myelin and axon repair following lesion of the central and peripheral nervous system, modulates brain inflammation with an isoform-specific effect.	15699400	Details
GRIN2A	SNP	rs9927924	PCR	MS	Phenotypic risk	we show associations between GRIN3A SNPs and phenotypic variation in NBV and NWMV in this first exploratory study	genetic association	22851457	Details
HLA-DQB1	Allele	NA	PCR	MS	Disease risk	We found that several HLA-DRB1 and DQB1 alleles were associated with MS.	Several studies have investigated the association of different HLA antigens with multiple sclerosis (MS).	29131543	Details
ICAM1	Exon 4 and exon 6	N/A	PCR	MS	N/A	ICAM-1 gene is not associated with multiple sclerosis in sardinian patients	Our data suggest that the increased expression of the ICAM-1 molecule observed in both blood and periplaque microvessels may be considered a consequence of the inflammatory process rather than the result of a genetic variation.	11081805	Details
HLA-DQB1	polymorphisms	DQB1*?	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
DBP	SNP	rs7041	PCR	MS	Disease risk	None of the polymorphisms showed any association with MS onset and progression.	Vitamin D binding protein (DBP) gene encodes for Gc, an α2 globulin that transports vitamin D metabolites in serum.	28284354	Details
MX1	SNP	rs2071430	PCR	MS	Treatment risk	No significant association was found between the MXA genotype at these two SNPs and clinical, MRI and MXA gene expression in MS patients treated with IFN-β therapy.	The anti-viral activity of MXA could contribute to control of viral infections, which can aggravate the symptoms of MS.	17126411	Details
HLA-DQA1	polymorphisms	DQA1*0501	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
HLA-DRB1	polymorphisms	DRB1*04	PCR	MS	Disease risk	A comparison of the transmission of HLA-DRB1 alleles in ASP and AUNN families	N/A	19098025	Details
HLA-DRB1	polymorphisms	DRB1*0403	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
TARDBP	mutation	Ala382Thr	PCR	MS	Disease risk	No difference in its frequency between MS patients and HCs was observed.	This protein is an ubiquitous and heterogeneous nuclear ribonucleoprotein involved in the prevention of the neurodegeneration by gene expression regulation, including RNA splicing and transport	26233805	Details
GRIN2A	SNP	rs6497658	PCR	MS	Phenotypic risk	we show associations between GRIN4A SNPs and phenotypic variation in NBV and NWMV in this first exploratory study	genetic association	22851457	Details
PHGDH	SNP	rs666930	PCR	MS	Disease risk	After FDR correction, we found a significant influence of the TT genotype of the rs666930 SNP (located in the phosphoglycerate dehydrogenase gene —PHGDH) on baseline MKO3 and MAP2K1 phosphorylation in MS patients	The changes in the activation of these kinases suggest that these pathways may represent therapeutic targets for modulation by kinase inhibitors.	31004050	Details
IL6	Allele	NA	PCR	MS	Treatment risk	In conclusion, the study of IL-6 -174 G>C polymorphism would allow the identification of patients lacking the C nucleo-tide on both alleles who are at risk of a more severe FLS, and may be addressed to a timely and stronger anti-inflammatory/antipyretic therapy for a more effective FLS prevention.	One of the most common adverse event of interferon beta (IFNβ) therapy for multiple sclero-sis is flu-like syndrome (FLS), which has been reportedly related to increased levels of cytokines such as interleukin 6 (IL-6) and tumor necrosis factor-alpha (TNF-α).	26285213	Details
MBP	1445 bp	N/A	PCR	MS	N/A	The differences between incidence of the three band pattern in the MS and the control group were significant at 1% level. Validation analysis furthermore support, the view that the 1445 bp PCR fragment is associated with MS.	N/A	7561955	Details
HLA-DPB1	polymorphisms	DPB1*0101	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
DBP	SNP	rs4588	PCR	MS	Disease risk	None of the polymorphisms showed any association with MS onset and progression.	Vitamin D binding protein (DBP) gene encodes for Gc, an α2 globulin that transports vitamin D metabolites in serum.	28284354	Details
MX1	SNP	rs17000900	PCR	MS	Treatment risk	No significant association was found between the MXA genotype at these two SNPs and clinical, MRI and MXA gene expression in MS patients treated with IFN-β therapy.	The anti-viral activity of MXA could contribute to control of viral infections, which can aggravate the symptoms of MS.	17126411	Details
HLA-DRB1	polymorphisms	DRB1*07	PCR	MS	Disease risk	A comparison of the transmission of HLA-DRB1 alleles in ASP and AUNN families	N/A	19098025	Details
HLA-DRB1	polymorphisms	DRB1*0404	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
GRIN2A	SNP	rs13338243	PCR	MS	Phenotypic risk	we show associations between GRIN5A SNPs and phenotypic variation in NBV and NWMV in this first exploratory study	genetic association	22851457	Details
IRF8	SNP	rs35929052	PCR	MS	Disease risk	the CT genotype of the rs35929052 SNP [located on IFN regulatory factor 8 (IRF8) gene, a key target of vitamin D receptor; refs. 11 and 12] had a significant influence on MAP2K1 phosphorylation after stimulation with vitamin D3	The changes in the activation of these kinases suggest that these pathways may represent therapeutic targets for modulation by kinase inhibitors.	31004050	Details
HLA-DRB1	Allele	NA	PCR	MS	Phenotypic risk	HLA DRB1*08 allele was related to a lower degree of disability.	Oligoclonal bands (OCB) may be associated with the genes of HLA complex, which allows to consider the possible interaction of genetic and immunological factors and its importance in the development and progression of multiple sclerosis (MS)	27515835	Details
Ace	SNP	rs1799752	PCR	MS	Disease risk	Analysis of genotype and allele frequencies of the mentioned variants in total MS patients compared with controls showed significant overrepresentation of the I allele of the rs1799752 in MS patients compared with healthy subjects (Adjusted P value=0.03, OR (95%CI)=1.28 (1.05–1.57).	The present study provides further evidences for the role of ACE in MS risk or response of patients to IFN-β treatment.	30218954	Details
HLA-DPB1	polymorphisms	DPB1*0201	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
DBP	SNP	rs2282679	PCR	MS	Disease risk	None of the polymorphisms showed any association with MS onset and progression.	Vitamin D binding protein (DBP) gene encodes for Gc, an α2 globulin that transports vitamin D metabolites in serum.	28284354	Details
IL4	SNP	rs2243250	PCR	MS	Disease risk	In dual luciferase assays of cultured Jurkat cells the cloned promoter comprising the 589 T allele leads to higher expression as compared to the respective construct with the C allele.	Dependent on the immunological situation, the 589 C/T variation may contribute to susceptibility for several autoimmune diseases by varying IL4 expression levels and hence modulation of the anti-inflammatory downregulation.	17855802	Details
HLA-DRB1	polymorphisms	DRB1*08	PCR	MS	Disease risk	A comparison of the transmission of HLA-DRB1 alleles in ASP and AUNN families	N/A	19098025	Details
HLA-DRB1	polymorphisms	DRB1*0405	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
IL7	SNP	rs1520333	PCR	MS	Disease risk	The frequency of the A/A genotype of rs1520333 in IL-7 gene of MS patients was observed dramatically lower than healthy controls, which reached the statistical difference. However, the allelic comparisons did not show the statistical significance.	Interleukin-7 (IL-7) was proved to be important in the pathogenesis of both diseases because of the roles it played in the differentiations of autoimmune lymphocytes.	26608987	Details
GRIN2A	SNP	rs1070484	PCR	MS	Phenotypic risk	we show associations between GRIN6A SNPs and phenotypic variation in NBV and NWMV in this first exploratory study	genetic association	22851457	Details
HLA-DRB1	Allele	NA	PCR	MS	Disease risk	Japanese MS patients and controls were examined for the distribution of HLA-DRBl, -DQAl, - DQBl, -DPAl and -DPB1 alleles using in vitro amplification of genomic DNA and probing with sequence-specific oligonucleotides. No significant difference in frequency of the examined alleles was observed among the two groups.	Recently, we reported that among Norwegian MS patients the disease may be more closely associated to certain combi- nations of DQAl and DQBl alleles (i.e. DQA1*0102, *0103, *0401 or *0501 in combi- nation with DQB1*0602, *0603, *0604, *0302 or *0303). In fact, 96% of Norwegian MS patients (compared to 60% of the controls) carry a combi- nation of these DQAl and DQBl alleles either in cis or in trans position, i.e. they may have DQaP heterodimers with similar peptide binding prop- erties (3).	1926126	Details
HLA-DPB1	polymorphisms	DPB1*0202	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
CYP27B1	SNP	rs4646536	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
HLA-DRB1	polymorphisms	DRB1*09	PCR	MS	Disease risk	A comparison of the transmission of HLA-DRB1 alleles in ASP and AUNN families	N/A	19098025	Details
HLA-DRB1	polymorphisms	DRB1*0406	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
CD58	SNP	rs1414273	PCR	MS	Disease risk	CD58 rs1414273A allele did not show any MS risk association in the replication Kuwaiti only population sample.CD58 rs1414273 genotypes were not significantly different with or without adjusting for sex.	N/A	32355262	Details
GRIN2A	SNP	rs3104703	PCR	MS	Phenotypic risk	we show associations between GRIN7A SNPs and phenotypic variation in NBV and NWMV in this first exploratory study	genetic association	22851457	Details
HFE	Gene polymorphisms	C282Y	PCR	MS	Disease risk	No significant association was found between HFE polymorphisms and disease susceptibility	It has been proposed that HFE gene polymorphisms could have a role in MS	20586792	Details
HLA-DQA1	Allele	NA	PCR	MS	Disease risk	Japanese MS patients and controls were examined for the distribution of HLA-DRBl, -DQAl, - DQBl, -DPAl and -DPB1 alleles using in vitro amplification of genomic DNA and probing with sequence-specific oligonucleotides. No significant difference in frequency of the examined alleles was observed among the two groups.	Recently, we reported that among Norwegian MS patients the disease may be more closely associated to certain combi- nations of DQAl and DQBl alleles (i.e. DQA1*0102, *0103, *0401 or *0501 in combi- nation with DQB1*0602, *0603, *0604, *0302 or *0303). In fact, 96% of Norwegian MS patients (compared to 60% of the controls) carry a combi- nation of these DQAl and DQBl alleles either in cis or in trans position, i.e. they may have DQaP heterodimers with similar peptide binding prop- erties (3).	1926126	Details
HLA-DPB1	polymorphisms	DPB1*0301	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
CYP27B1	SNP	rs4646537	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
HLA-DRB1	polymorphisms	DRB1*010	PCR	MS	Disease risk	A comparison of the transmission of HLA-DRB1 alleles in ASP and AUNN families	N/A	19098025	Details
HLA-DRB1	polymorphisms	DRB1*0407	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
TNFRSF1A	SNP	rs1800693	PCR	MS	Disease risk	TNFRSF1A rs1800693C allele did not sustain significant association with MS risk following adjustment for multiple testing.	TNFRSF1A is a membrane-bound and soluble receptor for tumor necrosis factor-alpha (TNFα) that plays a role in cellular survival, apoptosis and inflammation in the immune and nervous systems.	32355262	Details
HFE	Gene polymorphisms	H63D	PCR	MS	Disease risk	No significant association was found between HFE polymorphisms and disease susceptibility	It has been proposed that HFE gene polymorphisms could have a role in MS	20586792	Details
HLA-DQB1	Allele	NA	PCR	MS	Disease risk	Japanese MS patients and controls were examined for the distribution of HLA-DRBl, -DQAl, - DQBl, -DPAl and -DPB1 alleles using in vitro amplification of genomic DNA and probing with sequence-specific oligonucleotides. No significant difference in frequency of the examined alleles was observed among the two groups.	Recently, we reported that among Norwegian MS patients the disease may be more closely associated to certain combi- nations of DQAl and DQBl alleles (i.e. DQA1*0102, *0103, *0401 or *0501 in combi- nation with DQB1*0602, *0603, *0604, *0302 or *0303). In fact, 96% of Norwegian MS patients (compared to 60% of the controls) carry a combi- nation of these DQAl and DQBl alleles either in cis or in trans position, i.e. they may have DQaP heterodimers with similar peptide binding prop- erties (3).	1926126	Details
HLA-DPB1	polymorphisms	DPB1*0401	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
CYP27B1	SNP	rs703842	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
HLA-DRB1	polymorphisms	DRB1*11	PCR	MS	Disease risk	A comparison of the transmission of HLA-DRB1 alleles in ASP and AUNN families	N/A	19098025	Details
HLA-DRB1	polymorphisms	DRB1*0408	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
EVI5	SNP	rs11808092	PCR	MS	Disease risk	EVI5 rs11808092A allele showed significant MS risk association in the Kuwaiti population sample.In addition, EVI5 rs11808092 genotype association with female MS risk was stronger than in males.	N/A	32355262	Details
IL10	SNP	rs3135932	PCR	MS	Disease risk	our results suggest that S138G loss-of-function polymorphism of the IL-10R1 may be important risk factor in increasing susceptibility to MS.	loss-of-function variant	28225209	Details
HLA-DRB1	Gene polymorphisms	DRB1*03	PCR	MS	Disease risk	HLA-DRB1*03 allele group was overrepresented in NMO patients compared with healthy controls	these results indicate that the DRB profile of NMO patients is different from that observed for MS patients, further corroborating the distinction between NMO and MS	21396892	Details
HLA-DPB1	Allele	NA	PCR	MS	Disease risk	Japanese MS patients and controls were examined for the distribution of HLA-DRBl, -DQAl, - DQBl, -DPAl and -DPB1 alleles using in vitro amplification of genomic DNA and probing with sequence-specific oligonucleotides. No significant difference in frequency of the examined alleles was observed among the two groups.	Recently, we reported that among Norwegian MS patients the disease may be more closely associated to certain combi- nations of DQAl and DQBl alleles (i.e. DQA1*0102, *0103, *0401 or *0501 in combi- nation with DQB1*0602, *0603, *0604, *0302 or *0303). In fact, 96% of Norwegian MS patients (compared to 60% of the controls) carry a combi- nation of these DQAl and DQBl alleles either in cis or in trans position, i.e. they may have DQaP heterodimers with similar peptide binding prop- erties (3).	1926126	Details
MBP	polymorphisms	locus A	PCR	MS	Disease risk	Genetic susceptibility to multiple sclerosis in the Shanghai Chinese is not linked to the myelin basic protein gene microsatellite	N/A	16695982	Details
HLA-DPB1	polymorphisms	DPB1*0402	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
CYP27B1	SNP	rs8176345	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
HLA-DRB1	polymorphisms	DRB1*12	PCR	MS	Disease risk	A comparison of the transmission of HLA-DRB1 alleles in ASP and AUNN families	N/A	19098025	Details
HLA-DRB1	polymorphisms	DRB1*1101	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
MTHFR	SNP	rs1801131	PCR	MS	Disease risk	MTHFR rs1801131G allele significantly associated with MS risk.MTHFR rs1801131 genotype distribution differed between the two cohorts after adjusting for sex and age.	MTHFR is an enzyme involved in the conversion of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate and the missense variant rs1801131 (E429A) has been shown to cause decreased MTHFR enzymatic function and is associated with impaired folate metabolism and mild increases in homocysteine levels (hyperhomocysteinemia) that is reported to occur in MS patients.Sustained elevated homocysteine levels associate with cardiovascular disturbances that are thought to predispose to MS pathogenesis and progression.	32355262	Details
HLA-G	insertion/ deletion	N/A	PCR	MS	Disease risk	not only HLA-G 14 bp insertion/deletion polymorphism could be associated with expression rate of the HLA-G gene and its plasma level, but also could be considered as a risk factor for susceptibility to MS in our study population.	xpression rate of the HLA-G gene and its plasma level	26711580	Details
HLA-DRB1	Gene polymorphisms	DRB1*15	PCR	MS	Disease risk	In contrast, the HLA-DRB1*15 allele group was overrepresented in Brazilian MS patients	these results indicate that the DRB profile of NMO patients is different from that observed for MS patients, further corroborating the distinction between NMO and MS	21396892	Details
HLA-DPA1	Allele	NA	PCR	MS	Disease risk	Japanese MS patients and controls were examined for the distribution of HLA-DRBl, -DQAl, - DQBl, -DPAl and -DPB1 alleles using in vitro amplification of genomic DNA and probing with sequence-specific oligonucleotides. No significant difference in frequency of the examined alleles was observed among the two groups.	Recently, we reported that among Norwegian MS patients the disease may be more closely associated to certain combi- nations of DQAl and DQBl alleles (i.e. DQA1*0102, *0103, *0401 or *0501 in combi- nation with DQB1*0602, *0603, *0604, *0302 or *0303). In fact, 96% of Norwegian MS patients (compared to 60% of the controls) carry a combi- nation of these DQAl and DQBl alleles either in cis or in trans position, i.e. they may have DQaP heterodimers with similar peptide binding prop- erties (3).	1926126	Details
MBP	polymorphisms	locus B	PCR	MS	Disease risk	Genetic susceptibility to multiple sclerosis in the Shanghai Chinese is not linked to the myelin basic protein gene microsatellite	N/A	16695982	Details
HLA-DPB1	polymorphisms	DPB1*0501	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
CYP27B1	SNP	rs8176350	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
HLA-DRB1	polymorphisms	DRB1*13	PCR	MS	Disease risk	A comparison of the transmission of HLA-DRB1 alleles in ASP and AUNN families	N/A	19098025	Details
HLA-DRB1	polymorphisms	DRB1*1102	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
HLA-DRB3	Gene polymorphisms	DRB3	PCR	MS	Disease risk	DRB3 was overrepresented in NM	these results indicate that the DRB profile of NMO patients is different from that observed for MS patients, further corroborating the distinction between NMO and MS	21396892	Details
IL1B	Allele	NA	PCR	MS	Disease risk	A significant association was found for the IL-1β +3953 T allele [OR = 1.43, 95% CI (1.14–1.79), P value = 0.002, Pc = 0.01] and for IL-1β + 3953 T/T genotype and MS risk [OR = 1.92, 95% CI (1.25–2.96), P value = 0.005, Pc = 0.01]. Interestingly,the genotypes of the polymorphisms remained significant under recessive, co-recessive and dominant models.	The IL-1 gene family (IL-1α, IL-1β and IL-1RA) located in a cluster on the long arm of human chromosome 2 (2q13–14), have several recognized polymorphisms	26531703	Details
APOE	genotype	E3/E3	PCR	MS	Disease risk	We found no significant differences in genotype frequency between patients with multiple sclerosis and the control group.	Apolipoprotein E (ApoE) gene encodes an important protein in reforming injuries of central nervous system (CNS).	22973358	Details
HLA-DPB1	polymorphisms	DPB1*0601	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
VDR	SNP	rs2228570* (Fok1)	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
HLA-DRB1	polymorphisms	DRB1*14	PCR	MS	Disease risk	A comparison of the transmission of HLA-DRB1 alleles in ASP and AUNN families	N/A	19098025	Details
HLA-DRB1	polymorphisms	DRB1*1103	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
HLA-DRB5	Gene polymorphisms	DRB5*0101	PCR	MS	Disease risk	DRB5 overrepresented in MS patients	these results indicate that the DRB profile of NMO patients is different from that observed for MS patients, further corroborating the distinction between NMO and MS	21396892	Details
HLA-DRB1	Allele	NA	PCR	MS	Disease risk	Thus, DRBI * 1303 may serve as genetic risk factor for MS. Our study exemplifies the genetic heterogeneity in MS as there is a genetic effect of HLA on MS susceptibility in our low frequency DRBS*1SO0 patient.	A strong association exist between m ultiple sclerosis (MS) and the DRB1 *1SO1 haplotype, in most populations. Linkage of Multiple Sclerosis (MS) with the MHC or HLA region on chromosome 6p2I has previously been observed in DRBI*1SO positive MS families.	10618697	Details
APOE	genotype	E3/E4	PCR	MS	Disease risk	We found no significant differences in genotype frequency between patients with multiple sclerosis and the control group.	Apolipoprotein E (ApoE) gene encodes an important protein in reforming injuries of central nervous system (CNS).	22973358	Details
HLA-DPB1	polymorphisms	DPB1*0801	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
VDR	SNP	rs7975232 (Apa1)	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
HLA-DRB1	polymorphisms	DRB1*15	PCR	MS	Disease risk	The risk carried by HLA-DRB115 was increased in families with affected second-degree relatives (AUNN: OR 5 4.07) when compared with those consisting only first-degree relatives (ASP: OR 5 2.17), establishing heterogeneity of risk among HLADRB115 haplotypes based on whether collateral parental relatives are affected.	N/A	19098025	Details
HLA-DRB1	polymorphisms	DRB1*1104	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
APOE	polymorphism	N/A	PCR	MS	Treatment risk	We have not found, in our data, any influence of this gene in the RRMS response to INFbeta.	N/A	21163235	Details
VDR	gene polymorphisms	N/A	PCR	MS	Disease risk	he results indicate for the first time an association ofMS withVDRG polymorphism, which may be involved in pathogenesis of MS, or in the linkage disequilibrium of VDRG to another pathogenic gene loci	exerts an immunosuppressive effect	10465499	Details
HLA-DRB1	Gene polymorphisms	HLA-A*0301	PCR	MS	Disease risk	The HLA-A*0301 allele increases the risk of MS	these results indicate that the DRB profile of NMO patients is different from that observed for MS patients, further corroborating the distinction between NMO and MS	10746785	Details
HLA-DRB1	Allele	NA	PCR	MS	Disease risk	We did not detect an influence of the DR phenotype on disease course, age at onset/diagnosis, gender or familiarity. No association with Class I was detected in a random subset of patients and controls.	The association with HLA – DRB1 alleles was tested in 609 Continental Italian MS patients and 836 controls.	15081263	Details
APOE	genotype	E3/E2	PCR	MS	Disease risk	We found no significant differences in genotype frequency between patients with multiple sclerosis and the control group.	Apolipoprotein E (ApoE) gene encodes an important protein in reforming injuries of central nervous system (CNS).	22973358	Details
HLA-DPB1	polymorphisms	DPB1*0901	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
VDR	SNP	rs1544410 (Bsm1)	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
HLA-DRB1	polymorphisms	DRB1*16	PCR	MS	Disease risk	A comparison of the transmission of HLA-DRB1 alleles in ASP and AUNN families	N/A	19098025	Details
HLA-DRB1	polymorphisms	DRB1*1201	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
ZFAT	SNP	rs733254	PCR	MS	Disease risk	in an Arabian Gulf population, the ZFAT rs733254 polymorphism	N/A	27572828	Details
HLA-DRB1	Gene polymorphisms	HLA-A*0201	PCR	MS	Disease risk	The HLA-A*0301 allele increases the risk of MS	these results indicate that the DRB profile of NMO patients is different from that observed for MS patients, further corroborating the distinction between NMO and MS	10746785	Details
CFB	Allele	NA	PCR	MS	Phenotypic risk	There is a suggestion that the BF*S and Dw2+ alleles are more prevalent in chronic progressive patients, implying that in Dw2+ patients BF may influence the progression of the disease.	N/A	1797634	Details
APOE	genotype	E2/E4	PCR	MS	Disease risk	We found no significant differences in genotype frequency between patients with multiple sclerosis and the control group.	Apolipoprotein E (ApoE) gene encodes an important protein in reforming injuries of central nervous system (CNS).	22973358	Details
HLA-DPB1	polymorphisms	DPB1*1001	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
VDR	SNP	rs731236 (Taq1)	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
HLA-DRB1	polymorphisms	DRB1*17	PCR	MS	Disease risk	A comparison of the transmission of HLA-DRB1 alleles in ASP and AUNN families	N/A	19098025	Details
HLA-DRB1	polymorphisms	DRB1*1301	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
ZFAT	SNP	rs12557782	PCR	MS	Disease risk	ZFAT was associated with MS in women but not in men	genetic basis for the genderassociated susceptibility to MS	27572828	Details
CD40	SNP	rs1883832	PCR	MS	Disease risk	an C allele of rs6074022 polymorphism (CD40) was associated with a higher rate of MS progression	the genetic basis of susceptibility	23528589	Details
HLA-DRB1	SNP	rs3135388*A	PCR	MS	Disease risk	In this validation cohort, the correlation coefficient (r2) between rs3135388*A and HLA-DRB1*1501 was >0.94. Subsequently, applying the assay to a group of MS patients and controls from Belgium confirmed the association of HLA-DRB1*1501 and MS in this population	The human leukocyte antigen (HLA)-DRB1*1501 allele has long been established as the main genetic risk factor for multiple sclerosis (MS), and it therefore follows that stratification of study populations for this allele could aid in the identification of novel susceptibility genes and/or in establishing interactions.	18647361	Details
APOE	genotype	E2/E2	PCR	MS	Disease risk	We found no significant differences in genotype frequency between patients with multiple sclerosis and the control group.	Apolipoprotein E (ApoE) gene encodes an important protein in reforming injuries of central nervous system (CNS).	22973358	Details
HLA-DPB1	polymorphisms	DPB1*1101	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
VDR	SNP	rs11568820 (Cdx2)	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
HLA-DRB1	polymorphisms	DRB1*1302	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
ZFAT	SNP	rs2229857	PCR	MS	Disease risk	ZFAT was associated with MS in women but not in men	genetic basis for the genderassociated susceptibility to MS	27572828	Details
CD40	SNP	rs1535045	PCR	MS	Disease risk	and the TT genotype of rs1535045 was associated with a slower progression of MS and early MS onset	the genetic basis of susceptibility	23528589	Details
TRB	Allele	NA	PCR	MS	Phenotypic risk	Hierarchical clustering of the BV gene combinations, distin-guish three pMS auTCL groups, implying existence of up to three disease-related immune response patterns. These subgroup patterns may reflect different disease subclasses or alternatively they may suggest immune reactivity to different aetiological agents. Analyses of clonal-clustering patterns may potentially aid in subclassification of MS or in characterizing aetiological agents of this disease.	N/A	19740385	Details
HLA-DPB1	polymorphisms	DPB1*1301	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
VDR	SNP	rs10783219	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
SERPINE1	polymorphism	5G5G	PCR	MS	Disease risk	Women with RRMS had the most significant increase in 5G5G genotype frequency (OR, 2.48; p 5 0.028).	Moreover, 4G and 5G alleles bind a transcriptional activator, but the 5G allele also binds a repressor protein to an overlapping site, which leads to a decreased basal level of PAI-1 transcription.	10802801	Details
HLA-DRB1	polymorphisms	DRB1*1303	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
CTLA4	SNP	A49G	PCR	MS	Disease risk	There were no significant associations between the A49G genotype and risk of MS. There was a marginal trend towards increased risk of disease amongst AG heterozygotes compared to AA homozygotes.	Cytotoxic T lymphocyte-associated antigen-4 (CTLA-4; CD152) is expressed on activated CD4+ and CD8+ T cells and acts to down-regulate T cell function during co-stimulation.Changes in expression or function of the protein may influence the development of autoimmunity.Genetic CTLA-4 variants have been implicated in determining susceptibility to autoimmune diseases .	18378005	Details
ZFAT	SNP	rs9527281	PCR	MS	Disease risk	ZFAT was associated with MS in women but not in men	genetic basis for the genderassociated susceptibility to MS	27572828	Details
KIF1B	SNP	rs3135388	PCR	MS	Disease risk	A more benign course and a higher frequency of an T allele of rs3135388 was found in familial cases compared to sporadic case	the genetic basis of susceptibility	23528589	Details
TRA	Allele	NA	PCR	MS	Disease risk	To look for associations between these markers and autoimmune diseases,we have studied the restriction fragment length polymorphism distribution of the Pss I markers in patients with multiple sclerosis, myasthenia gravis, and Graves disease. Significant differences in the frequency of the polymorphic V. and C.markers were identified between patients and healthy individ-uals.	N/A	2915992	Details
CCL2	SNP	rs1024611	PCR	Inflammatory demyelinating disease (IDD)	Disease risk	N/A	five polymorphisms (rs1024611, rs2857656, rs3917887, rs4586, and rs13900) in this study were presented in the absolute LD, because we have not considered the normalized SNP selection process using various genome databases	24786287	Details
HLA-DPB1	polymorphisms	DPB1*1401	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
VDR	SNP	rs11168287	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
SERPINE1	polymorphism	4G4G	PCR	MS	Disease risk	Also, there was a decrease in frequency of the 4G4G genotype in women with MS (OR, 0.376; p 5 0.032).	Moreover, 4G and 5G alleles bind a transcriptional activator, but the 5G allele also binds a repressor protein to an overlapping site, which leads to a decreased basal level of PAI-1 transcription.	10802801	Details
HLA-DRB1	polymorphisms	DRB1*1305	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
ZFAT	SNP	rs11787532	PCR	MS	Disease risk	ZFAT was associated with MS in women but not in men	genetic basis for the genderassociated susceptibility to MS	27572828	Details
IL2	Allele	NA	PCR	MS	Disease risk	Our data demonstrated ?330 T IL2 allele provided major susceptibility to MS and HLA-DRB1* 1501 allele had an additive effect. In addi-tion, it seems that studies with larger sample size are required to bring about more authentic results. Our findings suggest that IL2 gene polymorphisms influence the susceptibility to MS in Iranian patients.	The purpose of this case–control study was to evaluate the frequencies and potential genetic susceptibility of the ?330 IL2 T and G alleles and HLA-DRB1*1501 allele in Iranian patients with multiple sclerosis (MS) compared to healthy controls.	24919928	Details
CCL2	SNP	rs2857656	PCR	Inflammatory demyelinating disease (IDD)	Disease risk	N/A	five polymorphisms (rs1024611, rs2857656, rs3917887, rs4586, and rs13900) in this study were presented in the absolute LD, because we have not considered the normalized SNP selection process using various genome databases	24786287	Details
HLA-DPB1	polymorphisms	DPB1*1501	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
VDR	SNP	rs11574024	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
KIF5A	SNP	rs1678542	PCR	MS	N/A	Association study of the different Tag-SNPs with multiple sclerosis	N/A	23160276	Details
HLA-DRB1	polymorphisms	DRB1*1405	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
ZFAT	SNP	rs7308076	PCR	MS	Disease risk	ZFAT was associated with MS in women but not in men	genetic basis for the genderassociated susceptibility to MS	27572828	Details
HLA-DRB1	Allele	NA	PCR	MS	Disease risk	Our data demonstrated ?330 T IL2 allele provided major susceptibility to MS and HLA-DRB1* 1501 allele had an additive effect. In addi-tion, it seems that studies with larger sample size are required to bring about more authentic results. Our findings suggest that IL2 gene polymorphisms influence the susceptibility to MS in Iranian patients.	The purpose of this case–control study was to evaluate the frequencies and potential genetic susceptibility of the ?330 IL2 T and G alleles and HLA-DRB1*1501 allele in Iranian patients with multiple sclerosis (MS) compared to healthy controls.	24919928	Details
CCL2	SNP	rs28730833	PCR	Inflammatory demyelinating disease (IDD)	Disease risk	N/A	five polymorphisms (rs1024611, rs2857656, rs3917887, rs4586, and rs13900) in this study were presented in the absolute LD, because we have not considered the normalized SNP selection process using various genome databases	24786287	Details
MTHFR	genotype	+ +	PCR	MS	Disease risk	However, the distribution of alleles and genotypes Was found to be close to identical in MS patients and healthy controls, regardless of subgroup analysis after clinical form Or HLA class 11 Phenotype.	N/A	24283912	Details
HLA-DPB1	polymorphisms	DPB1*1601	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
VDR	SNP	rs11574026	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
PRL	polymorphism	G-1149T	PCR	MS	Disease risk	No significant difference was observed when comparing the weighted mean of the gene frequencies of both MS (total MS) and both control pools (total control).	N/A	12559630	Details
KIF5A	SNP	rs2888334	PCR	MS	N/A	Association study of the different Tag-SNPs with multiple sclerosis	N/A	23160276	Details
HLA-DRB1	polymorphisms	DRB1*1402	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
IL6	SNP	rs1800796	PCR	MS	Disease risk	Patients with the 572 GC genotype overall showed a significantly higher median MSSS than did those with the GG genotype.	N/A	23202972	Details
ZFAT	SNP	rs2248202	PCR	MS	Disease risk	ZFAT was associated with MS in women but not in men	genetic basis for the genderassociated susceptibility to MS	27572828	Details
PON1	SNP	rs662	PCR	MS	Disease risk	According to our results, the PON1 and PON2 genotypes distribution did not differ between the MS patients and the controls	N/A	23487294	Details
CCL2	SNP	rs3917887	PCR	Inflammatory demyelinating disease (IDD)	Disease risk	N/A	five polymorphisms (rs1024611, rs2857656, rs3917887, rs4586, and rs13900) in this study were presented in the absolute LD, because we have not considered the normalized SNP selection process using various genome databases	24786287	Details
MTHFR	genotype	+ -	PCR	MS	Disease risk	However, the distribution of alleles and genotypes Was found to be close to identical in MS patients and healthy controls, regardless of subgroup analysis after clinical form Or HLA class 11 Phenotype.	N/A	24283912	Details
HLA-DPB1	polymorphisms	DPB1*1701	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
VDR	SNP	rs11574077	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
PRL	polymorphism	IVS3-C214T	PCR	MS	Disease risk	No significant difference was observed when comparing the weighted mean of the gene frequencies of both MS (total MS) and both control pools (total control).	N/A	12559630	Details
MEFV	mutation	E148Q	PCR	MS	Disease risk	In group 1, 19 MS patients (12.1%) tested positive for a mutation in the MEFV gene, mainly the E148Q (n=7) substitution.	N/A	22337722	Details
KIF5A	SNP	rs775249	PCR	MS	N/A	Association study of the different Tag-SNPs with multiple sclerosis	N/A	23160276	Details
HLA-DRB1	polymorphisms	DRB1*0701	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
RT1-Db1	haplotype	N/A	PCR	EAE	Disease risk	Susceptibility to EAE is inherited in a dominant fashion while susceptibility to SPR-EAE is not .The RT1av1 haplotype was associated with high susceptibility to EAE, development of severe/lethal ,relapses and a prolonged disease course.	N/A	9413257	Details
PON1	SNP	rs854560	PCR	MS	Disease risk	According to our results, the PON1 and PON2 genotypes distribution did not differ between the MS patients and the controls	N/A	23487294	Details
CCL2	SNP	rs2857657	PCR	Inflammatory demyelinating disease (IDD)	Disease risk	N/A	five polymorphisms (rs1024611, rs2857656, rs3917887, rs4586, and rs13900) in this study were presented in the absolute LD, because we have not considered the normalized SNP selection process using various genome databases	24786287	Details
MTHFR	genotype	- -	PCR	MS	Disease risk	However, the distribution of alleles and genotypes Was found to be close to identical in MS patients and healthy controls, regardless of subgroup analysis after clinical form Or HLA class 11 Phenotype.	N/A	24283912	Details
HLA-DPB1	polymorphisms	DPB1*1801	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
VDR	SNP	rs11574085	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
PRL	polymorphism	IVS3-G1220A	PCR	MS	Disease risk	No significant difference was observed when comparing the weighted mean of the gene frequencies of both MS (total MS) and both control pools (total control).	N/A	12559630	Details
MEFV	mutation	K695R	PCR	MS	Disease risk	In group 1, 19 MS patients (12.1%) tested positive for a mutation in the MEFV gene, mainly the E148Q (n=7) substitution.	N/A	22337722	Details
KIF5A	SNP	rs1678536	PCR	MS	N/A	Association study of the different Tag-SNPs with multiple sclerosis	N/A	23160276	Details
HLA-DRB1	polymorphisms	DRB1*0801	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
RT1-Db1	haplotype	N/A	PCR	EAE	Disease risk	The RT1av1 haplotype determines a characteristic type of inflammation with a high CD4/CD8 ratio and absence of mRNA for TGF-β and IL-10.	N/A	9413257	Details
PON1	SNP	rs705381	PCR	MS	Disease risk	According to our results, the PON1 and PON2 genotypes distribution did not differ between the MS patients and the controls	N/A	23487294	Details
CCR5	Allele	NA	PCR	MS	Phenotypic risk	However, age of onset was approximately 3 years later in patients carry-ing the CCR5D32 deletion (Pp0.018 after controlling for gender effects).	An un-derlying genetic susceptibility plays a clear role in the etiology of MS, likely acting in concert with an unde-fined environmental exposure. Full-genome screenings in multiplex MS families have identified several suscep-tibility regions, supporting a polygenic model for MS.	10803840	Details
CCL2	SNP	rs4586	PCR	Inflammatory demyelinating disease (IDD)	Disease risk	N/A	five polymorphisms (rs1024611, rs2857656, rs3917887, rs4586, and rs13900) in this study were presented in the absolute LD, because we have not considered the normalized SNP selection process using various genome databases	24786287	Details
MTHFR	allel	+	PCR	MS	Disease risk	However, the distribution of alleles and genotypes Was found to be close to identical in MS patients and healthy controls, regardless of subgroup analysis after clinical form Or HLA class 11 Phenotype.	N/A	24283912	Details
HLA-DPB1	polymorphisms	DPB1*1901	PCR	MS	Disease risk	The frequencies of all of the residues in each variable region of the amino acid sequences of DQβ and DPβ chains were not different between the MS patients and the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
VDR	SNP	rs11574114	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
PRL	polymorphism	IVS4-G2243A	PCR	MS	Disease risk	No significant difference was observed when comparing the weighted mean of the gene frequencies of both MS (total MS) and both control pools (total control).	N/A	12559630	Details
KIF5A	SNP	rs7313599	PCR	MS	N/A	Association study of the different Tag-SNPs with multiple sclerosis	N/A	23160276	Details
HLA-DRB1	polymorphisms	DRB1*0804	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
PON2	SNP	rs6954345	PCR	MS	Disease risk	According to our results, the PON1 and PON2 genotypes distribution did not differ between the MS patients and the controls	N/A	23487294	Details
CCL2	SNP	rs13900	PCR	Inflammatory demyelinating disease (IDD)	Disease risk	N/A	five polymorphisms (rs1024611, rs2857656, rs3917887, rs4586, and rs13900) in this study were presented in the absolute LD, because we have not considered the normalized SNP selection process using various genome databases	24786287	Details
MTHFR	allel	-	PCR	MS	Disease risk	However, the distribution of alleles and genotypes Was found to be close to identical in MS patients and healthy controls, regardless of subgroup analysis after clinical form Or HLA class 11 Phenotype.	N/A	24283912	Details
IL7R	SNP	rs987107	PCR	MS	Disease risk	All three SNPs confirmed association with multiple sclerosis.	IL7R is located on chromosome 5p13, a region occasionally suggested to be linked with multiple sclerosis.	17660816	Details
VDR	SNP	rs12581281	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
PRL	polymorphism	G671A	PCR	MS	Disease risk	No significant difference was observed when comparing the weighted mean of the gene frequencies of both MS (total MS) and both control pools (total control).	N/A	12559630	Details
PIP4K2C	SNP	rs1078109	PCR	MS	N/A	Association study of the different Tag-SNPs with multiple sclerosis	N/A	23160276	Details
HLA-DRB1	polymorphisms	DRB1*0901	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
KLC1	SNP	rs8702	PCR	MS	Disease risk	The homozygous variant KLC1 56836CC occurred significantly less frequently in the MS group than in the controls. The homozygous variant KLC1 56836CC proved to be protective as concerns the frequency of MS.	This genetic variant was found to be associated with cognitive disturbances and neurodegeneration, and it was presumed to affect the kinesin function. Kinesin serves as a main cytoskeleton motor protein by carrying mitochondria and the molecular apparatus of myelin basic protein synthesis.	17999208	Details
AGER	SNP	rs1800624	PCR	MS	Disease risk	Results indicate that rs1800624 polymorphism is not statistically significant in optic neuritis manifestation	the RAGE gene was selected as it is a part of the inflammation process	34338585	Details
TNFRSF1A	SNP	rs4149584	PCR	MS	Disease risk	Polymerase chain reaction–restriction fragment length poly‐ morphism method was used to genotype both TNFRSF1A polymorphisms in 541 MS patients and 724 healthy controls. Logistic regression analysis revealed a significantly increased risk of developing MS for the carriers of rs1800693 C allele (TC + CC vs.TT: pcorr = 0.005; OR = 1.61; 95% CI = 1.23–2.12), irrespective of sex and carriage of the major MS risk allele HLA‐DRB1*15:01. On the other hand, no association could be found between rs4149584 and MS risk (GA + AA vs. GG: pcorr = 1.00; OR = 1.25; 95% CI = 0.71–2.21)	tumour necrosis factor recep‐ tor superfamily member 1A (TNFRSF1A) gene on chromosome 12p13 was identified as a MS susceptibility gene in subjects of European an‐ cestry	30009568	Details
HLA-DRA	SNP	rs4935356	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
IL7R	SNP	rs987106	PCR	MS	Disease risk	All three SNPs confirmed association with multiple sclerosis.	IL7R is located on chromosome 5p13, a region occasionally suggested to be linked with multiple sclerosis.	17660816	Details
VDR	SNP	rs1540339	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
PRLR	polymorphism	C-524G	PCR	MS	Disease risk	No significant difference was observed when comparing the weighted mean of the gene frequencies of both MS (total MS) and both control pools (total control).	N/A	12559630	Details
ARHGEF25	SNP	rs7305391	PCR	MS	N/A	Association study of the different Tag-SNPs with multiple sclerosis	N/A	23160276	Details
HLA-DRB1	polymorphisms	DRB1*1001	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
CCR5	Deletion	Δ32 deletion allele	PCR	MS	Treatment risk	CCR5 Δ32 is not associated with lower disease activity in MS patients treated with natalizumab.	The expression of specific chemotactic factors in inflamed tissue helps guide specific subsets of immune cells expressing corresponding receptors to the site of inflammation.Perivascular inflammation is typical in MS lesions, and chemokines and their receptors are important for leucocyte recruitment into the CNS. In active, demyelinating brain lesions CCR5 expression has been observed on the surface of T helper type 1 (Th1) cells, regulatory T cells (T-reg) and monocytes. A deletion in the coding region of CCR5 termed CCR5 D32 gives rise to a non-functional receptor that is retained in the cell. CCR5 D32 heterozygous individuals have low expression of CCR5 protein and homozygous carriers of this mutation lack CCR5 on the cell surface.	23668375	Details
AGER	SNP	rs1800625	PCR	MS	Disease risk	RAGE rs1800625 AA genotype decreases the risk of optic neuritis	the RAGE gene was selected as it is a part of the inflammation process	34338585	Details
HLA-G	Allele	NA	PCR	MS	Disease risk	ur findings showed that the +3142 C>G, but not the 14 bp INS/DEL, polymorphism may constitute a genetic susceptibility factor to MS in the Tunisian population.	We aimed to investigate two main polymorphisms in the 3’ untranslated region (3’UTR) of the HLA-G gene [14 bp insertion/deletion (INS/DEL) and +3142 C>G] and to assess their impact on the soluble HLA-G (sHLA-G) production in patients with multiple sclerosis (MS).	27771469	Details
TNFRSF1A	SNP	rs1800693	PCR	MS	Disease risk	Polymerase chain reaction–restriction fragment length poly‐ morphism method was used to genotype both TNFRSF1A polymorphisms in 541 MS patients and 724 healthy controls. Logistic regression analysis revealed a significantly increased risk of developing MS for the carriers of rs1800693 C allele (TC + CC vs.TT: pcorr = 0.005; OR = 1.61; 95% CI = 1.23–2.12), irrespective of sex and carriage of the major MS risk allele HLA‐DRB1*15:01. On the other hand, no association could be found between rs4149584 and MS risk (GA + AA vs. GG: pcorr = 1.00; OR = 1.25; 95% CI = 0.71–2.21)	tumour necrosis factor recep‐ tor superfamily member 1A (TNFRSF1A) gene on chromosome 12p13 was identified as a MS susceptibility gene in subjects of European an‐ cestry	30009568	Details
HLA-DRA	SNP	rs3135390	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
IL7R	SNP	rs3194051	PCR	MS	Disease risk	All three SNPs confirmed association with multiple sclerosis.	IL7R is located on chromosome 5p13, a region occasionally suggested to be linked with multiple sclerosis.	17660816	Details
VDR	SNP	rs2189480	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
PRLR	polymorphism	T-435C	PCR	MS	Disease risk	No significant difference was observed when comparing the weighted mean of the gene frequencies of both MS (total MS) and both control pools (total control).	N/A	12559630	Details
PTPRC	mutation	C->G mutation in position 77 of exon 4	PCR	MS	Disease risk	This finding suggests a role, in at least a group of patients, for the PTPRC mutation in genetic susceptibility to MS.	N/A	12147336	Details
ARHGEF25	SNP	rs1564374	PCR	MS	N/A	Association study of the different Tag-SNPs with multiple sclerosis	N/A	23160276	Details
HLA-DQA1	polymorphisms	DQA1*0101	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
CCR5	Deletion	Δ32 deletion allele	PCR	MS	Phenotypic risk	We found lower MSSS scores in patients carrying CCR5 Δ32 compared with the remaining patients, which is consistent with previous studies reporting an association with a more favourable disease course.	The expression of specific chemotactic factors in inflamed tissue helps guide specific subsets of immune cells expressing corresponding receptors to the site of inflammation.Perivascular inflammation is typical in MS lesions, and chemokines and their receptors are important for leucocyte recruitment into the CNS. In active, demyelinating brain lesions CCR5 expression has been observed on the surface of T helper type 1 (Th1) cells, regulatory T cells (T-reg) and monocytes. A deletion in the coding region of CCR5 termed CCR5 D32 gives rise to a non-functional receptor that is retained in the cell. CCR5 D32 heterozygous individuals have low expression of CCR5 protein and homozygous carriers of this mutation lack CCR5 on the cell surface.	23668375	Details
VDR	Gene polymorphisms	FokI	PCR	MS	Disease risk	No significant difference between VDR polymorphisms and MS risk was detected	N/A	35848285	Details
ICAM1	Allele	NA	PCR	MS	Disease risk	Our analysis revealed no statistically significant asso-ciation of ICAM1 p o l y m o r p h i s m s w i t h r i s k o f M S d e v e l o p -ment in the Slovak population.	Infiltration of immune cells into CNS is one of the essential events in multiple sclerosis (MS) development.Adhesion molecules like the intercellular adhesion molecule 1 (ICAM-1) play critical role in this process.	28130760	Details
GC	gene polymorphisms	N/A	PCR	MS	Disease risk	In this study, antenatal or postnatal stressors may act as confounders. Maternal psychosocial stress during pregnancy has been shown to elicit increased maternal and fetal cortisol levels (54, 55). It is further associated with an increase in the offspring stress response, disturbed motor and structural brain development and an increased risk of cognitive, behavioral, and emotional problems in later life, such as autism spectrum disorders, ADHD, depression and schizophrenia (for reviews see (9, 55)). MS relapses are not only treated with GCs but also are a major psychological stressor. However, as relapses during pregnancy rarely go untreated, there is no realistic way of mitigating this confounder using an untreated MS control group. Due to the retrospective nature of this study, there is no reliable method to assess perceived psychological stress level beyond major stressful life events, at a minimum of 8 years in the past. The mother’s stress level during pregnancy is thus estimated using a questionnaire based on the Stress and Adversity Inventory (STRAIN) , which was adapted to this study’s context. Additionally, the children fill out a questionnaire regarding subjective and objective stress in the past 12 months	The aim of this study is to investigate the associations of fetal MP exposure in the context of MS relapse therapy with later cognitive function, brain development, stress sensitivity, and behavior	35557615	Details
HLA-DRA	SNP	rs4935354	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
IL7R	SNP	rs11567698	PCR	MS	Disease risk	Three of the tag SNPs showed significant association in the singlepoint analysis that survived after Bonferroni correction for multiple comparisons: rs2303137 (Puncorrected = 0.004, PBonferroni = 0.05), rs6871748 (Puncorrected = 0.003 and PBonferroni = 0.04) and the exon 6 nonsynonymous SNP rs6897932 (Puncorrected= 0.001, PBonferroni= 0.02).	IL7R is located on chromosome 5p13, a region occasionally suggested to be linked with multiple sclerosis.	17660816	Details
VDR	SNP	rs2107301	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
PRLR	polymorphism	IVS9-G1158A	PCR	MS	Disease risk	No significant difference was observed when comparing the weighted mean of the gene frequencies of both MS (total MS) and both control pools (total control).	N/A	12559630	Details
OS9	SNP	rs3825078	PCR	MS	N/A	Association study of the different Tag-SNPs with multiple sclerosis	N/A	23160276	Details
HLA-DQA1	polymorphisms	DQA1*0102	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
VDR	Gene polymorphisms	BsmI	PCR	MS	Disease risk	No significant difference between VDR polymorphisms and MS risk was detected	N/A	35848285	Details
ICAM1	SNP	rs5498	PCR	MS	Disease risk	however, patients with earlier onset of MS showed slightly higher frequencies of the homozygous G allele at rs5498 in comparison to other genotypes (P = 0 . 0 4 ) ,suggesting that GG carriers tend to induce MS at an earlier age.	Infiltration of immune cells into CNS is one of the essential events in multiple sclerosis (MS) development.Adhesion molecules like the intercellular adhesion molecule 1 (ICAM-1) play critical role in this process.	28130760	Details
TGFB3	gene polymorphisms	N/A	PCR	MS	Disease risk	The lower limits of the relative risk (Xs) possibly excluded for any candidate gene ranged from 1.3 to 2.8. Positive MLS values (up to 0.93) were observed for transforming growth factor beta 3 (TGFP3) in HLA DR15-associated families, suggesting a possible role for this growth factor in interaction with HLA. Conclusions: Oligodendrocyte growth factors do not play a significant role in MS genetic susceptibility, at least in the tested sample	kage of MS to human leukocyte antigen (HLA) DR15	9748021	Details
HLA-DRA	SNP	rs3177928	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
IL7R	SNP	rs11567701	PCR	MS	Disease risk	Three of the tag SNPs showed significant association in the singlepoint analysis that survived after Bonferroni correction for multiple comparisons: rs2303137 (Puncorrected = 0.004, PBonferroni = 0.05), rs6871748 (Puncorrected = 0.003 and PBonferroni = 0.04) and the exon 6 nonsynonymous SNP rs6897932 (Puncorrected= 0.001, PBonferroni= 0.02).	IL7R is located on chromosome 5p13, a region occasionally suggested to be linked with multiple sclerosis.	17660816	Details
VDR	SNP	rs2228572	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
PRLR	polymorphism	IVS10-A1870T	PCR	MS	Disease risk	No significant difference was observed when comparing the weighted mean of the gene frequencies of both MS (total MS) and both control pools (total control).	N/A	12559630	Details
OS9	SNP	rs701006	PCR	MS	N/A	Association study of the different Tag-SNPs with multiple sclerosis	N/A	23160276	Details
HLA-DQA1	polymorphisms	DQA1*0103	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
VDR	Gene polymorphisms	TaqI	PCR	MS	Disease risk	No significant difference between VDR polymorphisms and MS risk was detected	N/A	35848285	Details
HLA-DRB1	SNP	rs3135388	PCR	MS	Disease risk	Presence of the rs3135388 polymorphism tagging the major MS risk allele HLA-DRB1*15:01 allele was determined as well.	Infiltration of immune cells into CNS is one of the essential events in multiple sclerosis (MS) development.Adhesion molecules like the intercellular adhesion molecule 1 (ICAM-1) play critical role in this process.	28130760	Details
FGF2	gene polymorphisms	N/A	PCR	MS	Disease risk	The lower limits of the relative risk (Xs) possibly excluded for any candidate gene ranged from 1.3 to 2.8. Positive MLS values (up to 0.93) were observed for transforming growth factor beta 3 (TGFP3) in HLA DR15-associated families, suggesting a possible role for this growth factor in interaction with HLA. Conclusions: Oligodendrocyte growth factors do not play a significant role in MS genetic susceptibility, at least in the tested sample	kage of MS to human leukocyte antigen (HLA) DR15	9748021	Details
HLA-DRA	SNP	rs7194	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
IL7R	SNP	rs10461959	PCR	MS	Disease risk	Three of the tag SNPs showed significant association in the singlepoint analysis that survived after Bonferroni correction for multiple comparisons: rs2303137 (Puncorrected = 0.004, PBonferroni = 0.05), rs6871748 (Puncorrected = 0.003 and PBonferroni = 0.04) and the exon 6 nonsynonymous SNP rs6897932 (Puncorrected= 0.001, PBonferroni= 0.02).	IL7R is located on chromosome 5p13, a region occasionally suggested to be linked with multiple sclerosis.	17660816	Details
VDR	SNP	rs2238135	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
AGAP2	SNP	rs2301551	PCR	MS	N/A	Association study of the different Tag-SNPs with multiple sclerosis	N/A	23160276	Details
HLA-DQA1	polymorphisms	DQA1*0104	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
VDR	Gene polymorphisms	ApaI	PCR	MS	Disease risk	No significant difference between VDR polymorphisms and MS risk was detected	N/A	35848285	Details
CD40	Allele	NA	PCR	MS	Disease risk	In addition, the effect of the polymor-phism on CD40 ligand mRNA expression was assessed using PBMC from 54 MS patients and 22 controls. The phenotype frequencies for the CD40LG marker did not differ significantly between gender-conditioned intermediate-MS subgroups and controls, or between gender-conditioned disability octiles. Nor did the polymorphism appear to exert any significant effect on mRNA expression in either patients or controls.	In recent years, numerous reports have described the diverse roles of the CD40–CD40 ligand receptor–ligand pair .	11918631	Details
FGFR2	gene polymorphisms	N/A	PCR	MS	Disease risk	The lower limits of the relative risk (Xs) possibly excluded for any candidate gene ranged from 1.3 to 2.8. Positive MLS values (up to 0.93) were observed for transforming growth factor beta 3 (TGFP3) in HLA DR15-associated families, suggesting a possible role for this growth factor in interaction with HLA. Conclusions: Oligodendrocyte growth factors do not play a significant role in MS genetic susceptibility, at least in the tested sample	kage of MS to human leukocyte antigen (HLA) DR15	9748021	Details
HLA-DRA	SNP	rs7195	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
IL7R	SNP	rs3777090	PCR	MS	Disease risk	Three of the tag SNPs showed significant association in the singlepoint analysis that survived after Bonferroni correction for multiple comparisons: rs2303137 (Puncorrected = 0.004, PBonferroni = 0.05), rs6871748 (Puncorrected = 0.003 and PBonferroni = 0.04) and the exon 6 nonsynonymous SNP rs6897932 (Puncorrected= 0.001, PBonferroni= 0.02).	IL7R is located on chromosome 5p13, a region occasionally suggested to be linked with multiple sclerosis.	17660816	Details
VDR	SNP	rs2238136	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
MBP	allel	A	PCR	MS	Disease risk	When MS patients and healthy control subjects were stratified according to HLA-DRB1 phenotypes, a significant association of MS with MBP alleles was found only in the DR4- and DR5-positive subgroups.	N/A	12939427	Details
AGAP2	SNP	rs12307841	PCR	MS	N/A	Association study of the different Tag-SNPs with multiple sclerosis	N/A	23160276	Details
HLA-DQA1	polymorphisms	DQA1*0201	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
CCL20	SNP	rs6749704	PCR	MS	Disease risk	higher levels of CCL20 in patients that represent that the chemokine may play an important role in the pathogenesis ofMS	The rs6749704 polymorphismwas an associated SPMS pattern. The levels of CCL20 were not influenced by gender, disease pattern and treatment.	24395091	Details
CTLA4	Gene polymorphisms	-318 C/T	PCR	MS	Disease risk	We did not find any association with the promoter (-318 C/T) or intergenic CT60 SNPs in either of the disease cohorts	The CTLA-4 gene has receibed widespread attention as plausible candidate susceptibility gene for MS	17524498	Details
EIF2B1	Allele	NA	PCR	MS	Disease risk	We describe a VWM patient, homozygous carrier of this mutation, who presented with clinical characteristics compatible with multiple sclerosis (MS). Our goal was to check if G338A polymorph-ism is present in MS, particularly in patients with onset-associated neurological trauma.	Vanishing white matter (VWM) is a childhood leukoencephalopathy with central hypomyelination,white matter rarefaction, and cystic degeneration. Adult onset, variable phenotype, and high frequency characterize Arg113His mutation caused by G338A polymorphism associated with VWM.	17439913	Details
FGFR3	gene polymorphisms	N/A	PCR	MS	Disease risk	The lower limits of the relative risk (Xs) possibly excluded for any candidate gene ranged from 1.3 to 2.8. Positive MLS values (up to 0.93) were observed for transforming growth factor beta 3 (TGFP3) in HLA DR15-associated families, suggesting a possible role for this growth factor in interaction with HLA. Conclusions: Oligodendrocyte growth factors do not play a significant role in MS genetic susceptibility, at least in the tested sample	kage of MS to human leukocyte antigen (HLA) DR15	9748021	Details
HLA-DRA	SNP	rs1131541	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
IL7R	SNP	rs11567773	PCR	MS	Disease risk	Three of the tag SNPs showed significant association in the singlepoint analysis that survived after Bonferroni correction for multiple comparisons: rs2303137 (Puncorrected = 0.004, PBonferroni = 0.05), rs6871748 (Puncorrected = 0.003 and PBonferroni = 0.04) and the exon 6 nonsynonymous SNP rs6897932 (Puncorrected= 0.001, PBonferroni= 0.02).	IL7R is located on chromosome 5p13, a region occasionally suggested to be linked with multiple sclerosis.	17660816	Details
VDR	SNP	rs2239179	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
MBP	allel	B	PCR	MS	Disease risk	When MS patients and healthy control subjects were stratified according to HLA-DRB1 phenotypes, a significant association of MS with MBP alleles was found only in the DR4- and DR5-positive subgroups.	N/A	12939427	Details
AGAP2	SNP	rs12368653	PCR	MS	N/A	Association study of the different Tag-SNPs with multiple sclerosis	N/A	23160276	Details
HLA-DQA1	polymorphisms	DQA1*0301	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
CTLA4	Gene polymorphisms	intergenic CT60 SNPs	PCR	MS	Disease risk	We did not find any association with the promoter (-318 C/T) or intergenic CT60 SNPs in either of the disease cohorts	The CTLA-4 gene has receibed widespread attention as plausible candidate susceptibility gene for MS	17524498	Details
ADA	SNP	rs244072	PCR	MS	Disease risk	In MS patients, ADA SNP rs244072 is associated with CSF inflammation and disability.	The immune response homeostasis is crucially regulated by the activity of the enzyme adenosine deaminase (ADA), as evidenced in patients with genetic ADA deficiency and in those treated with cladribine tablets.	33007809	Details
PDGFA	gene polymorphisms	N/A	PCR	MS	Disease risk	The lower limits of the relative risk (Xs) possibly excluded for any candidate gene ranged from 1.3 to 2.8. Positive MLS values (up to 0.93) were observed for transforming growth factor beta 3 (TGFP3) in HLA DR15-associated families, suggesting a possible role for this growth factor in interaction with HLA. Conclusions: Oligodendrocyte growth factors do not play a significant role in MS genetic susceptibility, at least in the tested sample	kage of MS to human leukocyte antigen (HLA) DR15	9748021	Details
HLA-DRA	SNP	s7196	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
IL7R	SNP	rs1494555	PCR	MS	Disease risk	Three of the tag SNPs showed significant association in the singlepoint analysis that survived after Bonferroni correction for multiple comparisons: rs2303137 (Puncorrected = 0.004, PBonferroni = 0.05), rs6871748 (Puncorrected = 0.003 and PBonferroni = 0.04) and the exon 6 nonsynonymous SNP rs6897932 (Puncorrected= 0.001, PBonferroni= 0.02).	IL7R is located on chromosome 5p13, a region occasionally suggested to be linked with multiple sclerosis.	17660816	Details
VDR	SNP	rs2239181	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
MARCHF9	SNP	rs1048691	PCR	MS	N/A	Association study of the different Tag-SNPs with multiple sclerosis	N/A	23160276	Details
HLA-DQA1	polymorphisms	DQA1*0302	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
CTLA4	Gene polymorphisms	+49 A/G	PCR	MS	Disease risk	Our data highlight the CTLA4 +49 A/G and 3'UTR polymorphisms as potential modifiers of disease course in MS	The CTLA-4 gene has receibed widespread attention as plausible candidate susceptibility gene for MS	17524498	Details
SPP1	Allele	NA	PCR	MS	Disease risk	No association of OPN with susceptibility to MS was found in the Polish population.	Osteopontin (OPN) is a key cytokine involved in T-cell activation in multiple sclerosis (MS).	26785368	Details
IGF1R	gene polymorphisms	N/A	PCR	MS	Disease risk	The lower limits of the relative risk (Xs) possibly excluded for any candidate gene ranged from 1.3 to 2.8. Positive MLS values (up to 0.93) were observed for transforming growth factor beta 3 (TGFP3) in HLA DR15-associated families, suggesting a possible role for this growth factor in interaction with HLA. Conclusions: Oligodendrocyte growth factors do not play a significant role in MS genetic susceptibility, at least in the tested sample	kage of MS to human leukocyte antigen (HLA) DR15	9748021	Details
HLA-DRA	SNP	rs7197	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
IL7R	SNP	rs6897932	PCR	MS	Disease risk	Three of the tag SNPs showed significant association in the singlepoint analysis that survived after Bonferroni correction for multiple comparisons: rs2303137 (Puncorrected = 0.004, PBonferroni = 0.05), rs6871748 (Puncorrected = 0.003 and PBonferroni = 0.04) and the exon 6 nonsynonymous SNP rs6897932 (Puncorrected= 0.001, PBonferroni= 0.02).	IL7R is located on chromosome 5p13, a region occasionally suggested to be linked with multiple sclerosis.	17660816	Details
VDR	SNP	rs2239182	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
TSFM	SNP	rs6581155	PCR	MS	N/A	Association study of the different Tag-SNPs with multiple sclerosis	N/A	23160276	Details
HLA-DQA1	polymorphisms	DQA1*0303	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
CTLA4	Gene polymorphisms	3' UTR (AT(n))	PCR	MS	Disease risk	Our data highlight the CTLA4 +49 A/G and 3'UTR polymorphisms as potential modifiers of disease course in MS	The CTLA-4 gene has receibed widespread attention as plausible candidate susceptibility gene for MS	17524498	Details
SPP1	Allele	NA	PCR	MS	Phenotypic risk	No association of OPN with susceptibility to MS was found in the Polish population.	Osteopontin (OPN) is a key cytokine involved in T-cell activation in multiple sclerosis (MS).	26785368	Details
TRK-C	gene polymorphisms	N/A	PCR	MS	Disease risk	The lower limits of the relative risk (Xs) possibly excluded for any candidate gene ranged from 1.3 to 2.8. Positive MLS values (up to 0.93) were observed for transforming growth factor beta 3 (TGFP3) in HLA DR15-associated families, suggesting a possible role for this growth factor in interaction with HLA. Conclusions: Oligodendrocyte growth factors do not play a significant role in MS genetic susceptibility, at least in the tested sample	kage of MS to human leukocyte antigen (HLA) DR15	9748021	Details
HLA-DRA	SNP	rs1051336	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
IL7R	SNP	rs987107	PCR	MS	Disease risk	Three of the tag SNPs showed significant association in the singlepoint analysis that survived after Bonferroni correction for multiple comparisons: rs2303137 (Puncorrected = 0.004, PBonferroni = 0.05), rs6871748 (Puncorrected = 0.003 and PBonferroni = 0.04) and the exon 6 nonsynonymous SNP rs6897932 (Puncorrected= 0.001, PBonferroni= 0.02).	IL7R is located on chromosome 5p13, a region occasionally suggested to be linked with multiple sclerosis.	17660816	Details
VDR	SNP	rs2239185	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
HLA-DQA1	polymorphism	DQA1*0101	PCR	MS	Phenotypic risk	The alleles DQA1*0101 and DQA1*0102 occurred in a significantly higher proportion in the cases than in the Con-2 group.	N/A	10394051	Details
HLA-DQA1	polymorphisms	DQA1*0401	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
ESR1	Gene polymorphisms	PvuII	PCR	MS	Disease risk	Allelic and genotypic frequencies were not different between MS patients and population controls for either the PvuII or XbaI polymorphism	This result suggests that the association between a given disease and a genomic characterist	12098649	Details
TNF	Allele	NA	PCR	MS	Disease risk	The G allele in the examined position in tumor necrosis factor alpha might have a role as regards susceptibility in both remitting relapsing and primary progressive multiple sclerosis.	Tumor necrosis factor alpha, a proinflammatory cytokine, plays an important role in the clinical activity of relapsing–remitting multiple sclerosis and the development of progression.	20499285	Details
NRG1	gene polymorphisms	N/A	PCR	MS	Disease risk	The lower limits of the relative risk (Xs) possibly excluded for any candidate gene ranged from 1.3 to 2.8. Positive MLS values (up to 0.93) were observed for transforming growth factor beta 3 (TGFP3) in HLA DR15-associated families, suggesting a possible role for this growth factor in interaction with HLA. Conclusions: Oligodendrocyte growth factors do not play a significant role in MS genetic susceptibility, at least in the tested sample	kage of MS to human leukocyte antigen (HLA) DR15	9748021	Details
HLA-DRA	SNP	rs111471704	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
IL7R	SNP	rs987106	PCR	MS	Disease risk	Three of the tag SNPs showed significant association in the singlepoint analysis that survived after Bonferroni correction for multiple comparisons: rs2303137 (Puncorrected = 0.004, PBonferroni = 0.05), rs6871748 (Puncorrected = 0.003 and PBonferroni = 0.04) and the exon 6 nonsynonymous SNP rs6897932 (Puncorrected= 0.001, PBonferroni= 0.02).	IL7R is located on chromosome 5p13, a region occasionally suggested to be linked with multiple sclerosis.	17660816	Details
VDR	SNP	rs2239186	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
HLA-DQA1	polymorphism	DQA1*0102	PCR	MS	Phenotypic risk	The alleles DQA1*0101 and DQA1*0102 occurred in a significantly higher proportion in the cases than in the Con-2 group.	N/A	10394051	Details
HLA-DQA1	polymorphisms	DQA1*0501	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
ESR1	Gene polymorphisms	XbaI	PCR	MS	Disease risk	Allelic and genotypic frequencies were not different between MS patients and population controls for either the PvuII or XbaI polymorphism	This result suggests that the association between a given disease and a genomic characterist	12098649	Details
CD58	SNP	rs2300747G	PCR	MS	Disease risk	This protective rs2300747G allele is associated with a dose-dependent increase in CD58 mRNA expression in lymphoblastic cell lines (P ? 1.1 ? 10?10) and in peripheral blood mononuclear cells from MS subjects (P ? 0.0037).	Multiple sclerosis (MS) is an inflammatory disease of the central nervous system associated with demyelination and axonal loss. A whole genome association scan suggested that allelic variants in the CD58 gene region, encoding the costimulatory molecule LFA-3, are associated with risk of developing MS.	19237575	Details
EGFR	gene polymorphisms	N/A	PCR	MS	Disease risk	The lower limits of the relative risk (Xs) possibly excluded for any candidate gene ranged from 1.3 to 2.8. Positive MLS values (up to 0.93) were observed for transforming growth factor beta 3 (TGFP3) in HLA DR15-associated families, suggesting a possible role for this growth factor in interaction with HLA. Conclusions: Oligodendrocyte growth factors do not play a significant role in MS genetic susceptibility, at least in the tested sample	kage of MS to human leukocyte antigen (HLA) DR15	9748021	Details
HLA-DRA	SNP	rs1157343109	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
IL7R	SNP	rs3194051	PCR	MS	Disease risk	Three of the tag SNPs showed significant association in the singlepoint analysis that survived after Bonferroni correction for multiple comparisons: rs2303137 (Puncorrected = 0.004, PBonferroni = 0.05), rs6871748 (Puncorrected = 0.003 and PBonferroni = 0.04) and the exon 6 nonsynonymous SNP rs6897932 (Puncorrected= 0.001, PBonferroni= 0.02).	IL7R is located on chromosome 5p13, a region occasionally suggested to be linked with multiple sclerosis.	17660816	Details
VDR	SNP	rs2853559	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
HLA-DQA1	polymorphism	DQA1*0103	PCR	MS	Phenotypic risk	Gene frequencies for HLA DQA1* alleles in cases affected by MS and controls	N/A	10394051	Details
HLA-DQA1	polymorphisms	DQA1*0503	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
EIF2B5	SNP	rs843358	PCR	MS	Disease risk	We could not find statistically significant difference in the frequency of Ile587Val between MS patients and controls.	It is already known that alterations in Eukaryotic Translation Initiation Factor 2B (EIF2B) gene encoding the five subunits of eIF2B complex cause Vanishing White Matter (VWM) disease of the brain and emerging evidences have advocated certain resemblances between MS and VWM in terms of clinical and epidemiological characteristics, thus validating the association study between EIF2B and MS.EIF2B5 is a member of EIF2B 1–5 gene family which encodes the five non-identical subunits α, β, γ, δ and ε, respectively of eIF2B complex. eIF2B regulates translation initiation by converting eIF2-guanosine diphosphate (GDP) into eIF2-guanosine triphosphate (GTP), thus regenerating active eIF2 by exchange of GDP for GTP.This exchange step is very crucial in the regulation of translation initiation under different conditions.	26671108	Details
OAS1	SNP	rs10774671	PCR	MS	Disease risk	Haplotype but not single-marker analysis revealed an association of the haplotype created by the G allele at rs 10774671 and the A allele at rs 3741981 with the susceptibility to MS	OAS1 gene polymorphisms may confer susceptibility to MS or serve as markers of functional variants and suggest that OAS1 activity is involved in the etiology of the disease	17092260	Details
HLA-DRB1	Allele	NA	PCR	MS	Disease risk	Our evidence is c~'Lsistenc w/th the hypethesir,that one of the true disease susceptibility genes for MS lies elsewhere within the HLA region and in Northern European populations is found in significant association with Dgwl5 ~nd DQw6.	Seventy-one patients with multiple sclerosis (MS) were classified into four subgroups accord- ing to the clinical pattern of their disease; their HLA-DR and DQ polymorphisms were defined by serological methods and analysis ofTaq I digestion frggmants hybrid- izing with DRB, DQA, and DQB eDNA probes.	1683865	Details
ERBB2	gene polymorphisms	N/A	PCR	MS	Disease risk	The lower limits of the relative risk (Xs) possibly excluded for any candidate gene ranged from 1.3 to 2.8. Positive MLS values (up to 0.93) were observed for transforming growth factor beta 3 (TGFP3) in HLA DR15-associated families, suggesting a possible role for this growth factor in interaction with HLA. Conclusions: Oligodendrocyte growth factors do not play a significant role in MS genetic susceptibility, at least in the tested sample	kage of MS to human leukocyte antigen (HLA) DR15	9748021	Details
HLA-DRA	SNP	rs1041885	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
IL7R	SNP	rs10058453	PCR	MS	Disease risk	Three of the tag SNPs showed significant association in the singlepoint analysis that survived after Bonferroni correction for multiple comparisons: rs2303137 (Puncorrected = 0.004, PBonferroni = 0.05), rs6871748 (Puncorrected = 0.003 and PBonferroni = 0.04) and the exon 6 nonsynonymous SNP rs6897932 (Puncorrected= 0.001, PBonferroni= 0.02).	IL7R is located on chromosome 5p13, a region occasionally suggested to be linked with multiple sclerosis.	17660816	Details
VDR	SNP	rs3782905	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
HLA-DQA1	polymorphism	DQA1*0201	PCR	MS	Phenotypic risk	Gene frequencies for HLA DQA1* alleles in cases affected by MS and controls	N/A	10394051	Details
HLA-DQB1	polymorphisms	DQB1*0501	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
OAS1	SNP	rs3741981	PCR	MS	Disease risk	Haplotype but not single-marker analysis revealed an association of the haplotype created by the G allele at rs 10774671 and the A allele at rs 3741981 with the susceptibility to MS	OAS1 gene polymorphisms may confer susceptibility to MS or serve as markers of functional variants and suggest that OAS1 activity is involved in the etiology of the disease	17092260	Details
HLA-DQB1	Allele	NA	PCR	MS	Disease risk	Our evidence is c~'Lsistenc w/th the hypethesir,that one of the true disease susceptibility genes for MS lies elsewhere within the HLA region and in Northern European populations is found in significant association with Dgwl5 ~nd DQw6.	Seventy-one patients with multiple sclerosis (MS) were classified into four subgroups accord- ing to the clinical pattern of their disease; their HLA-DR and DQ polymorphisms were defined by serological methods and analysis ofTaq I digestion frggmants hybrid- izing with DRB, DQA, and DQB eDNA probes.	1683865	Details
NR5A1	gene polymorphisms	N/A	PCR	MS	Disease risk	The lower limits of the relative risk (Xs) possibly excluded for any candidate gene ranged from 1.3 to 2.8. Positive MLS values (up to 0.93) were observed for transforming growth factor beta 3 (TGFP3) in HLA DR15-associated families, suggesting a possible role for this growth factor in interaction with HLA. Conclusions: Oligodendrocyte growth factors do not play a significant role in MS genetic susceptibility, at least in the tested sample	kage of MS to human leukocyte antigen (HLA) DR15	9748021	Details
IL2RA	SNP	rs12722489	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
IL7R	SNP	rs6871748	PCR	MS	Disease risk	Three of the tag SNPs showed significant association in the singlepoint analysis that survived after Bonferroni correction for multiple comparisons: rs2303137 (Puncorrected = 0.004, PBonferroni = 0.05), rs6871748 (Puncorrected = 0.003 and PBonferroni = 0.04) and the exon 6 nonsynonymous SNP rs6897932 (Puncorrected= 0.001, PBonferroni= 0.02).	IL7R is located on chromosome 5p13, a region occasionally suggested to be linked with multiple sclerosis.	17660816	Details
VDR	SNP	rs3819545	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
HLA-DQA1	polymorphism	DQA1*0301	PCR	MS	Phenotypic risk	In contrast, the allele frequency of DQA1*0301 allele in cases was significantly lower than in Con-2.	N/A	10394051	Details
NOS2	genotype	n/n	PCR	MS	Disease risk	Results of a chi-squared analysis and a Fisher’s exact test revealed that allele and genotype distributions between cases and controls were not significantly different for the total population and for each subtype of MS.	N/A	15275951	Details
HLA-DQB1	polymorphisms	DQB1*0502	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
HLA-DRB1	Allele	NA	PCR	MS	Disease risk	Those patients from the Mediterranean area showed an association ctf MS with HLA-DR2 (p <0.001) and -DQwl (p <0.05), whilst in those from the Gulf there was an association with -DRw53 (p <0.02).	We have studied the HLA associations of MS patients in Arab patients from two re-gions.	2425452	Details
HLA-DRB1	gene polymorphisms	N/A	PCR	MS	Disease risk	We found a significant association with disease for the appearance of proline at position 11, arginine at position 13, and alanine at position 71 of HLA-DRb1. Surprisingly, we identified only residues preferentially expressed in the MS group that were related to HLA-DR2	relapsing-remitting versus primary chronic progressive MS, are influenced by the HLA-genotype	11082515	Details
IL2RA	SNP	rs917751277	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
IL7R	SNP	rs13169780	PCR	MS	Disease risk	Three of the tag SNPs showed significant association in the singlepoint analysis that survived after Bonferroni correction for multiple comparisons: rs2303137 (Puncorrected = 0.004, PBonferroni = 0.05), rs6871748 (Puncorrected = 0.003 and PBonferroni = 0.04) and the exon 6 nonsynonymous SNP rs6897932 (Puncorrected= 0.001, PBonferroni= 0.02).	IL7R is located on chromosome 5p13, a region occasionally suggested to be linked with multiple sclerosis.	17660816	Details
VDR	SNP	rs3890734	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
HLA-DQA1	polymorphism	DQA1*0401	PCR	MS	Phenotypic risk	Significant differences were shonw only in the distributions of the DQA1*0401 allele.	N/A	10394051	Details
NOS2	genotype	n/i	PCR	MS	Disease risk	Results of a chi-squared analysis and a Fisher’s exact test revealed that allele and genotype distributions between cases and controls were not significantly different for the total population and for each subtype of MS.	N/A	15275951	Details
HLA-DQB1	polymorphisms	DQB1*0503	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
CYP7A1	SNP	rs3808607	PCR	MS	Disease risk	Two known SNPs, -204A>C (rs3808607) and -469T>C (rs3824260), and a novel SNP (-208G>C) were identified in the 5'-UTR of CYP7A1. The -204A>C was in complete linkage with -469T>C and both were associated with NMO but not with MS	NMO and MS have different genetic risk factors	23740208	Details
HLA-DQB1	Allele	NA	PCR	MS	Disease risk	Those patients from the Mediterranean area showed an association ctf MS with HLA-DR2 (p <0.001) and -DQwl (p <0.05), whilst in those from the Gulf there was an association with -DRw53 (p <0.02).	We have studied the HLA associations of MS patients in Arab patients from two re-gions.	2425452	Details
CD4	SNP	rs7957426	PCR	MS	Disease risk	The result, including a total of 2640 MS patients and 2194 controls shows no significant association with CD4 and LAG3 and MS. We conclude that these genes are of minor importance in regard of genetic predisposition to the MS	We have investigated the genetic involvement of the CD4 and the LAG3 genes, two appealing candidates for MS due to their suggested role in MS pathology	17020785	Details
IL2RA	SNP	rs992067421	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
IL7R	SNP	rs6870944	PCR	MS	Disease risk	Three of the tag SNPs showed significant association in the singlepoint analysis that survived after Bonferroni correction for multiple comparisons: rs2303137 (Puncorrected = 0.004, PBonferroni = 0.05), rs6871748 (Puncorrected = 0.003 and PBonferroni = 0.04) and the exon 6 nonsynonymous SNP rs6897932 (Puncorrected= 0.001, PBonferroni= 0.02).	IL7R is located on chromosome 5p13, a region occasionally suggested to be linked with multiple sclerosis.	17660816	Details
VDR	SNP	rs4237855	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
NOS2	genotype	i/i	PCR	MS	Disease risk	Results of a chi-squared analysis and a Fisher’s exact test revealed that allele and genotype distributions between cases and controls were not significantly different for the total population and for each subtype of MS.	N/A	15275951	Details
HLA-DQB1	polymorphisms	DQB1*0609	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
CYP24A1	SNP	rs2762943	PCR	MS	Disease risk	The presence of the rs2762943 risk allele had no significant impact on disease activity and disability outcomes during follow-颅up. However, risk allele carriers were younger at disease onset (p = 0.04).	is associated with lower 1,25(OH)2D levels and a heightened pro-颅inflammatory environment in MS patients.	37183562	Details
CYP7A1	SNP	rs3824260	PCR	MS	Disease risk	Two known SNPs, -204A>C (rs3808607) and -469T>C (rs3824260), and a novel SNP (-208G>C) were identified in the 5'-UTR of CYP7A1. The -204A>C was in complete linkage with -469T>C and both were associated with NMO but not with MS	NMO and MS have different genetic risk factors	23740208	Details
HLA-DRB1	Allele	NA	PCR	MS	Disease risk	Those patients from the Mediterranean area showed an association ctf MS with HLA-DR2 (p <0.001) and -DQwl (p <0.05), whilst in those from the Gulf there was an association with -DRw53 (p <0.02).	We have studied the HLA associations of MS patients in Arab patients from two re-gions.	2425452	Details
CD4	SNP	rs10774450	PCR	MS	Disease risk	The result, including a total of 2640 MS patients and 2194 controls shows no significant association with CD4 and LAG3 and MS. We conclude that these genes are of minor importance in regard of genetic predisposition to the MS	We have investigated the genetic involvement of the CD4 and the LAG3 genes, two appealing candidates for MS due to their suggested role in MS pathology	17020785	Details
IL2RA	SNP	rs959264277	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
IL7R	SNP	rs2303137	PCR	MS	Disease risk	Three of the tag SNPs showed significant association in the singlepoint analysis that survived after Bonferroni correction for multiple comparisons: rs2303137 (Puncorrected = 0.004, PBonferroni = 0.05), rs6871748 (Puncorrected = 0.003 and PBonferroni = 0.04) and the exon 6 nonsynonymous SNP rs6897932 (Puncorrected= 0.001, PBonferroni= 0.02).	IL7R is located on chromosome 5p13, a region occasionally suggested to be linked with multiple sclerosis.	17660816	Details
VDR	SNP	rs4328262	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
NOS2	allel	n	PCR	MS	Disease risk	Results of a chi-squared analysis and a Fisher’s exact test revealed that allele and genotype distributions between cases and controls were not significantly different for the total population and for each subtype of MS.	N/A	15275951	Details
HLA-DQB1	polymorphisms	DQB1*0602	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
TLR3	SNP	rs116729895	PCR	MS	Disease risk	The alignment identified multiple substitution mutations across the five exons of the TLR3 gene (rs116729895, rs3775296, rs377529, rs3775290, rs3775291, rs376735334 and rs73873710). A significant difference was observed in the allele distribution of rs3775291 (Leu412Phe) between MS patients and HC, whereby the minor allele was detected in 38.9% ofMS patients versus 11% of HC (Fisher's exact test, p=0.021).	TLR recognition and various cytotoxic and immunoregulatory functions	31177052	Details
CYP7A1	SNP	-208G>C	PCR	MS	Disease risk	Two known SNPs, -204A>C (rs3808607) and -469T>C (rs3824260), and a novel SNP (-208G>C) were identified in the 5'-UTR of CYP7A1. The -204A>C was in complete linkage with -469T>C and both were associated with NMO but not with MS	NMO and MS have different genetic risk factors	23740208	Details
CD4	SNP	rs3782736	PCR	MS	Disease risk	The result, including a total of 2640 MS patients and 2194 controls shows no significant association with CD4 and LAG3 and MS. We conclude that these genes are of minor importance in regard of genetic predisposition to the MS	We have investigated the genetic involvement of the CD4 and the LAG3 genes, two appealing candidates for MS due to their suggested role in MS pathology	17020785	Details
IL2RA	SNP	rs11597542	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
VDR	SNP	rs4516035	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
IL1A	SNP	rs1800587	PCR	MS	N/A	There wasn’t any association between IL-1A 889, IL1RN VNTR and IL-1B +3953 genotypes and MS risk.	It has been shown that the IL-1A 889 (1/2) polymorphism leads to high expression of IL-1A gene, which may affect progression of MS disease.	23594042	Details
NOS2	allel	i	PCR	MS	Disease risk	Results of a chi-squared analysis and a Fisher’s exact test revealed that allele and genotype distributions between cases and controls were not significantly different for the total population and for each subtype of MS.	N/A	15275951	Details
HLA-DQB1	polymorphisms	DQB1*0603	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
TLR3	SNP	rs3775296	PCR	MS	Disease risk	The alignment identified multiple substitution mutations across the five exons of the TLR3 gene (rs116729895, rs3775296, rs377529, rs3775290, rs3775291, rs376735334 and rs73873710). A significant difference was observed in the allele distribution of rs3775291 (Leu412Phe) between MS patients and HC, whereby the minor allele was detected in 38.9% ofMS patients versus 11% of HC (Fisher's exact test, p=0.022).	TLR recognition and various cytotoxic and immunoregulatory functions	31177052	Details
CCL14	SNP	rs854680	PCR	MS	Disease risk	After correction for multiple testing, only PG28 (rs854680) remains significant in the SLE group	This follow up study aims to refine the roles of previously suggested candidate genes (CC chemokine ligands or CCLs) in multiple sclerosis (MS), and to test these markers in another autoimmune disorder, systemic lupus erythematosus (SLE)	18602166	Details
IL2RA	SNP	rs140860467	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
VDR	SNP	rs4760648	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
IL-1RN	SNP	rs 16944	PCR	MS	N/A	There wasn’t any association between IL-1A 889, IL1RN VNTR and IL-1B +3953 genotypes and MS risk.	However they suggested that the IL-1Ra VNTR polymorphism might be associated with bout-onset MS subtype.	23594042	Details
IL1RN	polymorphisms	A1/A1	PCR	MS	Phenotypic risk	The A1/A1 genotype of the anti-inflammatory cytokine interleukin 1 receptor antagonist (IL-1Ra) polymorphism was more frequent in 339 Italian MS patients than in healthy controls (HCs).	N/A	10371542	Details
HLA-DQB1	polymorphisms	DQB1*0604	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
TLR3	SNP	rs377529	PCR	MS	Disease risk	The alignment identified multiple substitution mutations across the five exons of the TLR3 gene (rs116729895, rs3775296, rs377529, rs3775290, rs3775291, rs376735334 and rs73873710). A significant difference was observed in the allele distribution of rs3775291 (Leu412Phe) between MS patients and HC, whereby the minor allele was detected in 38.9% ofMS patients versus 11% of HC (Fisher's exact test, p=0.023).	TLR recognition and various cytotoxic and immunoregulatory functions	31177052	Details
VDR	SNP	rs10735810	PCR	MS	Disease risk	Although our findings suggest a weak association between VDR SNP FokI and the MS risk in women	vitamin D acts through the vitamin D receptor (VDR), association of single nucleotide polymorphisms (SNPs) in the VDR gene might account for variations in the MS risk within populations	25376135	Details
RGS7	Allele	NA	PCR	MS	Disease risk	In this follow-up study, we saturated the region with ~700 SNPs (average spacing of 10kb per SNP) in search of disease associated variation within this region. We found preliminary evidence to suggest that common variation within the RGS7 locus may be involved in disease susceptibility.	Our own second-generation genome-wide linkage study identified a handful of non-MHC regions with suggestive linkage.	19626040	Details
CCL14	SNP	rs16971802	PCR	MS	Disease risk	PG28 (rs854680) is located 1641bp from the 3′ UTR of the CCL14 gene. PG29 (rs16971802) is a non-synonymous SNP (C → T) in exon II of the CCL14 gene, which changes glutamine → lysine at protein level. Further extension of this haplotype into the CCL4 gene (PG28–PG29–PG30–PG31–PG32) also reveals a significant association	This follow up study aims to refine the roles of previously suggested candidate genes (CC chemokine ligands or CCLs) in multiple sclerosis (MS), and to test these markers in another autoimmune disorder, systemic lupus erythematosus (SLE)	18602166	Details
IL2RA	SNP	rs17149458	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
VDR	SNP	rs4760655	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
IL1B	SNP	rs 1143634	PCR	MS	N/A	However, we have found significantly decreased frequency of IL-1B 511 genotype in MS patients compared to controls.	It is important for IL-1β gene expression.	23594042	Details
IL1RN	polymorphisms	A1/A2	PCR	MS	Phenotypic risk	A more aggressive disease course was also associated with A11 genotypes and might reflect the reduced ability of mononuclear cell cultures of A11 HCs to produce IL-1Ra.	N/A	10371542	Details
HLA-DQB1	polymorphisms	DQB1*0605	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
TLR3	SNP	rs3775290	PCR	MS	Disease risk	The alignment identified multiple substitution mutations across the five exons of the TLR3 gene (rs116729895, rs3775296, rs377529, rs3775290, rs3775291, rs376735334 and rs73873710). A significant difference was observed in the allele distribution of rs3775291 (Leu412Phe) between MS patients and HC, whereby the minor allele was detected in 38.9% ofMS patients versus 11% of HC (Fisher's exact test, p=0.024).	TLR recognition and various cytotoxic and immunoregulatory functions	31177052	Details
MEFV	Gene mutations	M694V	PCR	MS	Disease risk	There were statistically significant differences of the MEFV gene mutation carrier rates and allele frequencies between MS patients and healthy controls	Mediterranean fever (MEFV) gene has already been identified as being responsible for FMF.	23297013	Details
HLA-A	Allele	NA	PCR	MS	Disease risk	We identified significant effects on MS susceptibility of HLA-A*2 (OR: 0.51; P = 0.05) and A*3 (OR: 2.85; P = 0.005), and two coding polymorphisms in the MOG gene (V145I: P = 0.01, OR: 2.2; V142L: P = 0.04,OR: 0.45) after full conditioning on HLA-DRB1.	This study is an extension to previously published work that has linked variation in the human leukocyte antigen (HLA) class I region with susceptibility to multiple sclerosis (MS) in Australians from the Island State of Tasmania.	17971048	Details
IL7R	SNP	rs6897932	PCR	MS	Disease risk	This outcome indicates that other types of genome variants should be required for the development and progression of MS, which may vary among populations and is consistent with a complex disease model in which multiple genes and environmental factors contribute to the phenotype	these data suggest that carriers of the ‘C’ allele at rs6897932 produce less membrane-bound IL7RA protein compared with carriers of the ‘T’ allele, leading to a further increase of the soluble form of IL7RA	18721276	Details
IL2RA	SNP	rs12722490	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
SLC11A1	allele	2	PCR	MS	Disease risk	Statistically significant differences in allelic distribution were observed between the patient and control samples drawn from the same population (P , 0.01).	The many cellular functions dependent on iron and other metal ions as cofactors may explain the complex role of NRAMP1 in infectious and autoimmune disease.	11358358	Details
VDR	SNP	rs7136534	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
IL1B	SNP	IL-1 RN variable number tandom repeat (VNTR)	PCR	MS	N/A	There wasn’t any association between IL-1A 889, IL1RN VNTR and IL-1B +3953 genotypes and MS risk.	It is important implications in immune health.	23594042	Details
IL1RN	polymorphisms	A2/A2	PCR	MS	Phenotypic risk	The A1/A1 genotype was more (and the A2/A2 less) represented among MS patients than it was in HCs.	N/A	10371542	Details
HLA-DQB1	polymorphisms	DQB1*0606	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
MPO	myeloperoxidase promoter polymorphism	position 1856–2629 of MPO	PCR	MS	N/A	We did not find an association with gender, age at onset, susceptibility to, or the course and severity of MS in a population-based sample of 122 patients from Olmsted County	Myeloperoxidase (MPO) generates hypochlorous acid and other reactive oxygen intermediates leading to tissue damage	10742562	Details
TLR3	SNP	rs3775291	PCR	MS	Disease risk	There appears to be a possible association between the TLR3 missense mutation rs3775291 and multiple sclerosis, which might be attributed to changes in the TLR3 functional properties	TLR recognition and various cytotoxic and immunoregulatory functions	31177052	Details
MEFV	Gene mutations	M680I	PCR	MS	Disease risk	There were statistically significant differences of the MEFV gene mutation carrier rates and allele frequencies between MS patients and healthy controls	Mediterranean fever (MEFV) gene has already been identified as being responsible for FMF.	23297013	Details
TRB	Allele	NA	PCR	MS	Phenotypic risk	These data indicate that certain MS patients have abnormal TCRBV gene expression. Such abnormalities are caused by polyclonal expansions of T lymphocyte subpopulations that use the same TCRBV gene families, are unstable and preferentially observed early in the course of the disease	Such abnormalities are caused by polyclonal expansions of T lymphocyte subpopulations that use the same TCRBV gene families, are unstable and preferentially observed early in the course of the disease	9626994	Details
GPC1	SNP	rs9523787	PCR	MS	Disease risk	Thus, this study supports that MS susceptibility at 13q31–32 may localize to the Glypican-5 gene, which should lead to further fine-mapping, replication and functional studies of this gene	MSassociated variants have been reported at both HLA and non-HLA loci, the latter including chromosome 13q31–32 and the Glypican-5 and Glypican-6 genes	20692050	Details
IL2RA	SNP	rs3118470	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
SLC11A1	allele	3	PCR	MS	Disease risk	Comparison of Allelic Distribution between South African MS Patients (22 Males, 82 Females) and Controls	The many cellular functions dependent on iron and other metal ions as cofactors may explain the complex role of NRAMP1 in infectious and autoimmune disease.	11358358	Details
VDR	SNP	rs739837	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
CTLA4	polymorphism	-1722 T C	PCR	MS	Disease risk	The distribution of -1722 T C, -1661 A G, -318 C T and +49 A G (TACA) haplotype, from the contrary, was observed to be significantly increased among controls.	Following surface expression, CTLA4 is reported to suppress T cell function by inducing indoleamine 2,3-dioxygenase metabolism in dendritic cells.	19737153	Details
GSTP1	allele	lle	PCR	MS	Disease risk	Associations between the allele frequencies of GSTP1, OGG1 and XRCC1 gene polymorphisms and the risk of Multiple Sclerosis (MS).	Since polymorphisms in DNA repair genes can result in reduced DNA repair capacity	26562193	Details
HLA-DQB1	polymorphisms	DQB1*0201	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
MT-ND1	polymorphism	Nt 4216 T>C	PCR	MS	Disease risk	Our results indicated that the prevalence of ND1 gene variations was significantly higher in patients than in healthy controls.We failed to detect Nt 4216 T>C variations in the control group.	The mitochondria can play fundamental roles in the pathogenesis of MS.Complex I deficiency may contribute to disease susceptibility in MS.	25172194	Details
IL10	diallelic polymorphism	position –1082 in the IL10 promotor	PCR	MS	N/A	We analysed this diallelic polymorphism in patients with multiple sclerosis but did not find any association between a certain –1082 IL10 genotype and susceptibility to or severity of multiple sclerosis	N/A	10683520	Details
TLR3	SNP	rs376735334	PCR	MS	Disease risk	The alignment identified multiple substitution mutations across the five exons of the TLR3 gene (rs116729895, rs3775296, rs377529, rs3775290, rs3775291, rs376735334 and rs73873710). A significant difference was observed in the allele distribution of rs3775291 (Leu412Phe) between MS patients and HC, whereby the minor allele was detected in 38.9% ofMS patients versus 11% of HC (Fisher's exact test, p=0.026).	TLR recognition and various cytotoxic and immunoregulatory functions	31177052	Details
MEFV	Gene mutations	V726A	PCR	MS	Disease risk	There were statistically significant differences of the MEFV gene mutation carrier rates and allele frequencies between MS patients and healthy controls	Mediterranean fever (MEFV) gene has already been identified as being responsible for FMF.	23297013	Details
LOC102724971	Allele	NA	PCR	MS	Phenotypic risk	Our results demonstrate that in MS CSF, there is a high frequency of clonally expanded B cells that have properties of postgerminal center memory or antibody-forming lymphocytes.	The cerebrospinal fluid (CSF) of multiple sclerosis (MS) patients is characterized by increased concentrations of immunoglobulin (Ig), which on electrophoretic analysis shows restricted heterogeneity (oligoclonal bands).	9727074	Details
GPC1	SNP	rs7333912	PCR	MS	Disease risk	Thus, this study supports that MS susceptibility at 13q31–32 may localize to the Glypican-5 gene, which should lead to further fine-mapping, replication and functional studies of this gene	MSassociated variants have been reported at both HLA and non-HLA loci, the latter including chromosome 13q31–32 and the Glypican-5 and Glypican-6 genes	20692050	Details
IL2RA	SNP	rs78556477	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
SLC11A1	allele	5	PCR	MS	Disease risk	Comparison of Allelic Distribution between South African MS Patients (22 Males, 82 Females) and Controls	The many cellular functions dependent on iron and other metal ions as cofactors may explain the complex role of NRAMP1 in infectious and autoimmune disease.	11358358	Details
VDR	SNP	rs757343	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
CTLA4	polymorphism	-1661 A G	PCR	MS	Disease risk	The distribution of -1722 T C, -1661 A G, -318 C T and +49 A G (TACA) haplotype, from the contrary, was observed to be significantly increased among controls.	Following surface expression, CTLA4 is reported to suppress T cell function by inducing indoleamine 2,4-dioxygenase metabolism in dendritic cells.	19737153	Details
GSTP1	allele	Val	PCR	MS	Disease risk	Associations between the allele frequencies of GSTP1, OGG1 and XRCC1 gene polymorphisms and the risk of Multiple Sclerosis (MS).	Since polymorphisms in DNA repair genes can result in reduced DNA repair capacity	26562193	Details
HLA-DQB1	polymorphisms	DQB1*0301	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
MT-ND2	polymorphism	Nt 5153 A>G	PCR	MS	Disease risk	Our results indicated that the prevalence of ND2 gene variations was significantly higher in patients than in healthy controls.The Nt 5153 A>G variations in males of the patient group were significantly higher than those in the males of the control group.The Nt 5153 A>G variations in the females of the patient group were significantly higher than those in the females of the control group .	The mitochondria can play fundamental roles in the pathogenesis of MS.Complex I deficiency may contribute to disease susceptibility in MS.	25172194	Details
CTLA4	Polymorphism of the CTLA-4 gene	dinucleotide microsatelite (AT)	PCR	MS	N/A	Polymorphism of the CTLA-4 gene (chromosome 2q33) could thus have effects upon the immune response	the CTLA-4 exon 1 gene polymorphism at position 49, which results in amino acid exchange (Thr to Ala) in the leader sequence10	12894875	Details
TLR3	SNP	rs73873710	PCR	MS	Disease risk	The alignment identified multiple substitution mutations across the five exons of the TLR3 gene (rs116729895, rs3775296, rs377529, rs3775290, rs3775291, rs376735334 and rs73873710). A significant difference was observed in the allele distribution of rs3775291 (Leu412Phe) between MS patients and HC, whereby the minor allele was detected in 38.9% ofMS patients versus 11% of HC (Fisher's exact test, p=0.027).	TLR recognition and various cytotoxic and immunoregulatory functions	31177052	Details
MEFV	Gene mutations	E148Q	PCR	MS	Disease risk	There were statistically significant differences of the MEFV gene mutation carrier rates and allele frequencies between MS patients and healthy controls	Mediterranean fever (MEFV) gene has already been identified as being responsible for FMF.	23297013	Details
CYTH4	Allele	NA	PCR	MS	Disease risk	indicating a dominant and protective effect for the longer alleles against neurodegeneration.	The longest tetra-nucleotide repeat identified in a human gene core promoter belongs to the CYTH4 gene. This GTTT-repeat is specific to Hominidae and Old World monkeys, and the shortest allele of this repeat, (GTTT)6, i s l i n k e d w i t h n e u r a l dysfunction and type I bipolar disorder in human.	25823437	Details
GPC1	SNP	rs17267815	PCR	MS	Disease risk	Thus, this study supports that MS susceptibility at 13q31–32 may localize to the Glypican-5 gene, which should lead to further fine-mapping, replication and functional studies of this gene	MSassociated variants have been reported at both HLA and non-HLA loci, the latter including chromosome 13q31–32 and the Glypican-5 and Glypican-6 genes	20692050	Details
IL2RA	SNP	rs41294925	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
MBP	allele	1.29 kb	PCR	MS	Disease risk	Our data indicate that in the Italian population the myelin basic protein gene does not play a major role in conferring genetic susceptibility to multiple sclerosis.	a significant association between MS and a multiallelic polymorphism identified upstream from the 5" end of the human MBP gene on chromosome 18.	7530769	Details
VDR	SNP	rs886441	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
CTLA4	polymorphism	-318 C T	PCR	MS	Disease risk	The distribution of -1722 T C, -1661 A G, -318 C T and +49 A G (TACA) haplotype, from the contrary, was observed to be significantly increased among controls.	Following surface expression, CTLA4 is reported to suppress T cell function by inducing indoleamine 2,5-dioxygenase metabolism in dendritic cells.	19737153	Details
OGG1	allele	Ser	PCR	MS	Disease risk	Associations between the allele frequencies of GSTP1, OGG1 and XRCC1 gene polymorphisms and the risk of Multiple Sclerosis (MS).	Since polymorphisms in DNA repair genes can result in reduced DNA repair capacity	26562193	Details
HLA-DQB1	polymorphisms	DQB1*0302	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
MT-ND3	polymorphism	Nt 10142 C>T	PCR	MS	Disease risk	Our results indicated that the prevalence of ND3 gene variations was significantly higher in patients than in healthy controls.We failed to detect Nt 10142 C>T variations in the control group.	The mitochondria can play fundamental roles in the pathogenesis of MS.Complex I deficiency may contribute to disease susceptibility in MS.	25172194	Details
HLA-DRB1	multiallelic polymorphisms	DRB1*1501	PCR	MS	Disease risk	Evidence supporting the existence of linkage between MS susceptibility and the HLA class II loci DRB1, DQA1 and DQB1 was provided using two non-parametric tests, affected sib-pair analysis, and affected-pedigree-member (APM) analy- sis.	MS susceptibility is conferred by HLA class II alleles according to a low-penetrance autoso- mal recessive mode of inheritance.	8556305	Details
MEFV	Gene mutations	P369S	PCR	MS	Disease risk	There were statistically significant differences of the MEFV gene mutation carrier rates and allele frequencies between MS patients and healthy controls	Mediterranean fever (MEFV) gene has already been identified as being responsible for FMF.	23297013	Details
CCR2	SNP	rs1799864	PCR	MS	Disease risk	In conclusion,our results suggest that CCR2 +190 G/A polymorphism may increase the susceptibility to MS, but its action seems to be restricted to individuals who do not possess the major risk allele HLA-DRB1*15:01.	C–C chemokine receptor 2 (CCR2) is one of the key players involved in the transmigration of mononuclear cells into the central nervous system (CNS) and subsequent development of multiple sclerosis (MS).	25604634	Details
GPC1	SNP	rs12876985	PCR	MS	Disease risk	Thus, this study supports that MS susceptibility at 13q31–32 may localize to the Glypican-5 gene, which should lead to further fine-mapping, replication and functional studies of this gene	MSassociated variants have been reported at both HLA and non-HLA loci, the latter including chromosome 13q31–32 and the Glypican-5 and Glypican-6 genes	20692050	Details
IL2RA	SNP	rs12722491	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
MBP	allele	1.27 kb	PCR	MS	Disease risk	Our data indicate that in the Italian population the myelin basic protein gene does not play a major role in conferring genetic susceptibility to multiple sclerosis.	a significant association between MS and a multiallelic polymorphism identified upstream from the 5" end of the human MBP gene on chromosome 18.	7530769	Details
VDR	SNP	rs987849	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
CTLA4	polymorphism	+49 A G	PCR	MS	Disease risk	The distribution of -1722 T C, -1661 A G, -318 C T and +49 A G (TACA) haplotype, from the contrary, was observed to be significantly increased among controls.	Following surface expression, CTLA4 is reported to suppress T cell function by inducing indoleamine 2,6-dioxygenase metabolism in dendritic cells.	19737153	Details
OGG1	allele	Cys	PCR	MS	Disease risk	Associations between the allele frequencies of GSTP1, OGG1 and XRCC1 gene polymorphisms and the risk of Multiple Sclerosis (MS).	Since polymorphisms in DNA repair genes can result in reduced DNA repair capacity	26562193	Details
HLA-DQB1	polymorphisms	DQB1*0303	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
MT-ND4	polymorphism	Nt 11353 T>C, Nt 11935 T>C, Nt 12062 C>T	PCR	MS	Disease risk	Our results indicated that the prevalence of ND4 gene variations was significantly higher in patients than in healthy controls.We failed to detect Nt 11353 T>C, Nt 11935 T>C variations in the control group.The Nt 12062 C>T variation in the females of the case group was significantly higher than that in males whereas, there is no significant difference in the prevalence of remnant variations between males and females of the case group.The Nt 12062 C>T variations in the females of the patient group were significantly higher than those in the females of the control group .	The mitochondria can play fundamental roles in the pathogenesis of MS.Complex I deficiency may contribute to disease susceptibility in MS.	25172194	Details
HLA-DQA1	multiallelic polymorphisms	DQA1*0102	PCR	MS	Disease risk	Evidence supporting the existence of linkage between MS susceptibility and the HLA class II loci DRB1, DQA1 and DQB1 was provided using two non-parametric tests, affected sib-pair analysis, and affected-pedigree-member (APM) analy- sis.	MS susceptibility is conferred by HLA class II alleles according to a low-penetrance autoso- mal recessive mode of inheritance.	8556305	Details
IL32	Allele	NA	PCR	MS	Disease risk	IL-32 gene promoter polymorphism is a genetic risk factor for multiple sclerosis patients particularly women.	Although the exact cause of multiple sclerosis is not known, there are a number of factors involved mainly environmental and genetic factors. The present study was done to determine association between IL-32 gene promoter polymorphism and IL-32 levels with multiple sclerosis.	35131367	Details
IRF5	SNP	rs4728142	PCR	MS	Disease risk	The combined analysis of available datasets yielded an effect size on MS with odds ratio (OR)MantelHaenszel 1.14 (Po0.002) for the IRF5 polymorphisms rs4728142 and rs3807306	1 IRF pathways also participate in the regulation of the antiviral innate response.2 IRF5-induced innate antiviral responses appear to result in a broad alteration of the transcriptional profile of cellular genes.3,4 IRF5 is expressed mainly in lymphocytes and dendritic cells, but it is induced in other cells in response to type I interferon (IFN)5	20861862	Details
IL2RA	SNP	rs550805995	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
MBP	allele	1.25 kb	PCR	MS	Disease risk	Our data indicate that in the Italian population the myelin basic protein gene does not play a major role in conferring genetic susceptibility to multiple sclerosis.	a significant association between MS and a multiallelic polymorphism identified upstream from the 5" end of the human MBP gene on chromosome 18.	7530769	Details
VDR	SNP	rs2283342	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
CTLA4	SNP	TACA	PCR	MS	Disease risk	The distribution of -1722 T C, -1661 A G, -318 C T and +49 A G (TACA) haplotype, from the contrary, was observed to be significantly increased among controls.	Following surface expression, CTLA4 is reported to suppress T cell function by inducing indoleamine 2,7-dioxygenase metabolism in dendritic cells.	19737153	Details
XRCC1	allele	Arg	PCR	MS	Disease risk	Associations between the allele frequencies of GSTP1, OGG1 and XRCC1 gene polymorphisms and the risk of Multiple Sclerosis (MS).	Since polymorphisms in DNA repair genes can result in reduced DNA repair capacity	26562193	Details
HLA-DQB1	polymorphisms	DQB1*0402	PCR	MS	Disease risk	We observed no significant differences of the cytokine production in relation to disease status or any HLA polymorphism.	N/A	11470147	Details
MT-ND5	polymorphism	Nt 13042 G>A, Nt 13708 G>A	PCR	MS	Disease risk	Our results indicated that the prevalence of ND5 gene variations was significantly higher in patients than in healthy controls.We failed to detect Nt 13708 G>A variations in the control group. The Nt 13042 G>A variations in males of the patient group were significantly higher than those in the males of the control group.The Nt 13042 G>A variations in the females of the patient group were significantly higher than those in the females of the control group .	The mitochondria can play fundamental roles in the pathogenesis of MS.Complex I deficiency may contribute to disease susceptibility in MS.	25172194	Details
HLA-DQB1	multiallelic polymorphisms	DQB1*0602	PCR	MS	Disease risk	Evidence supporting the existence of linkage between MS susceptibility and the HLA class II loci DRB1, DQA1 and DQB1 was provided using two non-parametric tests, affected sib-pair analysis, and affected-pedigree-member (APM) analy- sis.	MS susceptibility is conferred by HLA class II alleles according to a low-penetrance autoso- mal recessive mode of inheritance.	8556305	Details
CD24	Allele	NA	PCR	MS	Disease risk	This study showed a strong association between the presence of AA genotype in the 1626 polymorphism of the CD24 gene and the risk of disease progression in MS patients.	Previous reports have shown that CD24 gene polymorphisms have an important role in the risk of development and progression of multiple sclerosis	21641619	Details
IRF5	SNP	rs3807306	PCR	MS	Disease risk	The combined analysis of available datasets yielded an effect size on MS with odds ratio (OR)MantelHaenszel 1.14 (Po0.002) for the IRF5 polymorphisms rs4728142 and rs3807306	1 IRF pathways also participate in the regulation of the antiviral innate response.2 IRF5-induced innate antiviral responses appear to result in a broad alteration of the transcriptional profile of cellular genes.3,4 IRF5 is expressed mainly in lymphocytes and dendritic cells, but it is induced in other cells in response to type I interferon (IFN)5	20861862	Details
IL2RA	SNP	rs12722621	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
MBP	allele	1.23 kb	PCR	MS	Disease risk	Our data indicate that in the Italian population the myelin basic protein gene does not play a major role in conferring genetic susceptibility to multiple sclerosis.	a significant association between MS and a multiallelic polymorphism identified upstream from the 5" end of the human MBP gene on chromosome 18.	7530769	Details
VDR	SNP	rs2254210	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
CTLA4	SNP	TACG	PCR	MS	Disease risk	List of observed haplotypes among patients and healthy controls and the statistical analyses are summarized in Table 3.	Following surface expression, CTLA4 is reported to suppress T cell function by inducing indoleamine 2,8-dioxygenase metabolism in dendritic cells.	19737153	Details
XRCC1	allele	Gln	PCR	MS	Disease risk	Associations between the allele frequencies of GSTP1, OGG1 and XRCC1 gene polymorphisms and the risk of Multiple Sclerosis (MS).	Since polymorphisms in DNA repair genes can result in reduced DNA repair capacity	26562193	Details
MT-ND6	polymorphism	Nt 14179 G>A	PCR	MS	Disease risk	The frequency of Nt 14179 G>A variation in ND6 gene was significantly higher in the control group compared with the patients.	The mitochondria can play fundamental roles in the pathogenesis of MS.Complex I deficiency may contribute to disease susceptibility in MS.	25172194	Details
BDNF	SNP	rs56164415	PCR	MS	Disease risk	No association was found for any of the SNPs to disease susceptibility or any clinical or demographic parameters including sex, age at onset, disease course, disease severity and cognitive impairment.	Brain-derived neurotrophic factor (BDNF) has been proposed a protective role in multiple sclerosis (MS) in several studies	22341604	Details
HMGB	SNP	DELINSCrs146076135	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
MBP	allele	1.20kb	PCR	MS	Disease risk	Our data indicate that in the Italian population the myelin basic protein gene does not play a major role in conferring genetic susceptibility to multiple sclerosis.	a significant association between MS and a multiallelic polymorphism identified upstream from the 5" end of the human MBP gene on chromosome 18.	7530769	Details
CYP24A1	SNP	rs1555439	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
CTLA4	SNP	TGCG	PCR	MS	Disease risk	List of observed haplotypes among patients and healthy controls and the statistical analyses are summarized in Table 3.	Following surface expression, CTLA4 is reported to suppress T cell function by inducing indoleamine 2,9-dioxygenase metabolism in dendritic cells.	19737153	Details
GSTP1	genotype	Ile/Ile	PCR	MS	Disease risk	Associations between genotype frequencies of GSTP1, OGG1 and XRCC1 gene polymorphisms and the risk of Multiple Sclerosis (MS).	Since polymorphisms in DNA repair genes can result in reduced DNA repair capacity	26562193	Details
NOTCH4	SNP	rs422951	PCR	MS	Disease risk	This NOTCH4 missense mutation decreased the risk for developing MS in Japanese, but did not affect clinical features of those who had already developed the disease	missense mutation	23549433	Details
IL2RA	SNP	rs2104286	PCR	MS	Disease risk	We have identified allele specific methylation of the CpG-site located in intron 1 that is perturbed by the rs2104286 SNP in CD8+ T cells from genotype-selected healthy subjects (HS).	N/A	34386002	Details
HSPA4	SNP	rs2227956	PCR	MS	Disease risk	We reported a strong association between rs2227956 polymorphism and MS risk, which is independent from the association with HSP70-2 rs1061581, and a significant link between hsp70-hom protein expression and MS severity.	Immune-mediated and neurodegenerative mechanisms are involved in multiple sclerosis (MS). Growing evi-dences highlight the role of HSP70 genes in the susceptibility of some neurological diseases.	27609295	Details
HMGB	SNP	DELINSTrs201945336	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
TNFRSF1A	mutation	R92Q	PCR	MS	Disease risk	We found a marginally non-significant increase in the frequency of mutants carriers in the cohort of patients (5.5%) as compared to the control group (1.3%), P = 0.1; OR = 4.5; 95% CI 0.53–40.3.	It is caused by mutations in the tumor necrosis factor (TNF) receptor superfamily 1A (TNFRSF1A; MIM 191190) gene, which encodes the TNFa 55-kd receptor.	21567205	Details
CYP24A1	SNP	rs1570669	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
CTLA4	SNP	TGCA	PCR	MS	Disease risk	Preliminary results showed significant increase of +49 G allele and )1661 AG genotype, as well as TGCA haplotype among patients than controls.	Following surface expression, CTLA4 is reported to suppress T cell function by inducing indoleamine 2,10-dioxygenase metabolism in dendritic cells.	19737153	Details
GSTP1	genotype	Ile/Val	PCR	MS	Disease risk	Associations between genotype frequencies of GSTP1, OGG1 and XRCC1 gene polymorphisms and the risk of Multiple Sclerosis (MS).	Since polymorphisms in DNA repair genes can result in reduced DNA repair capacity	26562193	Details
KCNA3	SNP	rs2821557	PCR	MS	Disease risk	In conclusion, accelerated MS progression in C allele carriers is likely linked to enhanced Kv1.3-mediated accumulation of pathogenic CXCR3+ TEM cells and exacerbated neuroinflammation.	accumulation of pathogenic CXCR3+ TEM cells and exacerbated neuroinflammation	32056271	Details
CTLA4	Allele	NA	PCR	MS	Disease risk	Our results suggest that the CTLA-4 + 49 alone is not associated with overall susceptibility to MS, but may be important in clinical subsets of patients and/or may interact epistatically with other gene polymorphisms.	Susceptibility to multiple sclerosis (MS) may be influenced by the interaction of several genes within a biological pathway. T cell activation and costimulation may be potentially important in MS pathogenesis.	14975605	Details
HMGB	SNP	rs111892138	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
TNFRSF1A	mutation	R92Q	PCR	MS	Phenotype risk	We found no differences in MS clinical features, treatment response and tolerability between carriers and non-carriers.	It is caused by mutations in the tumor necrosis factor (TNF) receptor superfamily 1A (TNFRSF1A; MIM 191190) gene, which encodes the TNFa 55-kd receptor.	21567205	Details
CYP24A1	SNP	rs2181874	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
CTLA4	SNP	TATA	PCR	MS	Disease risk	List of observed haplotypes among patients and healthy controls and the statistical analyses are summarized in Table 3.	Following surface expression, CTLA4 is reported to suppress T cell function by inducing indoleamine 2,11-dioxygenase metabolism in dendritic cells.	19737153	Details
GSTP1	genotype	Val/Val	PCR	MS	Disease risk	Associations between genotype frequencies of GSTP1, OGG1 and XRCC1 gene polymorphisms and the risk of Multiple Sclerosis (MS).	Since polymorphisms in DNA repair genes can result in reduced DNA repair capacity	26562193	Details
NR3C1	SNP	rs6189/6190	PCR	MS	Disease risk	We demonstrated significant differences in distribution of genotype, allele and haplotype frequencies of rs6189, rs41423247 and rs55829688 between the study groups	the long non-coding RNA (lncRNA) growth arrest specific 5 (GAS5) interacts with GR through binding to the DNA-binding domain (DBD) region and reduces GR transcriptional activity	31724909	Details
HLA-DRB1	Allele	NA	PCR	MS	Disease risk	Analysis taking into account the known HLA-DR2 association identified two additional potential linkage regions on chromosomes 7q21–22 and 13q33–34	Several genomic screens have been undertaken to locate such genes, but have not provided consistent gene localization, except for the MHC on chromosome 6p21 and a locus on chromosome 19q13.	12217953	Details
HMGB	SNP	DELINSArs200308321	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
TNFRSF1A	mutation	R92Q	PCR	MS	Treatment risk	We found no differences in MS clinical features, treatment response and tolerability between carriers and non-carriers.	It is caused by mutations in the tumor necrosis factor (TNF) receptor superfamily 1A (TNFRSF1A; MIM 191190) gene, which encodes the TNFa 55-kd receptor.	21567205	Details
CYP24A1	SNP	rs2209314	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
CTLA4	SNP	CACA	PCR	MS	Disease risk	List of observed haplotypes among patients and healthy controls and the statistical analyses are summarized in Table 3.	Following surface expression, CTLA4 is reported to suppress T cell function by inducing indoleamine 2,12-dioxygenase metabolism in dendritic cells.	19737153	Details
GSTP1	genotype	Ile/Val +Val/Val	PCR	MS	Disease risk	Associations between genotype frequencies of GSTP1, OGG1 and XRCC1 gene polymorphisms and the risk of Multiple Sclerosis (MS).	Since polymorphisms in DNA repair genes can result in reduced DNA repair capacity	26562193	Details
TLR3	polymorphism	1377	PCR	MS	Disease risk	There was significant difference in genotype and allele distribution of TLR3c.1377 polymorphism between the MS patients and the controls, and the MS patients with T allele had a lower risk.	N/A	20197609	Details
NR3C1	SNP	rs56149945	PCR	MS	Disease risk	We demonstrated significant differences in distribution of genotype, allele and haplotype frequencies of rs6189, rs41423247 and rs55829689 between the study groups	the long non-coding RNA (lncRNA) growth arrest specific 5 (GAS6) interacts with GR through binding to the DNA-binding domain (DBD) region and reduces GR transcriptional activity	31724909	Details
TAP2	Allele	NA	PCR	MS	Disease risk	The results of this study exclude TAP2 as a locus for a necessary MS/MHC gene but indicate that an MS gene carried by the DRBl* 1501, DQAl * 0102, DQBl* 0602 haplotype could reside centromeric of DQ.	Polymorphism of the TAP2 gene locus, situated approximately 150 kb centromeric to the MHC class II loci HLA-DR, DQ was examined in 100 Australian patients with relapsing/remitting multiple sclerosis (MS), in 100 random controls and in 37 selected HLA-DRBl* 1501-positive controls.	7797612	Details
HMGB	SNP	DELINSGAAGrs149637108	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
AGER	genotype	374 T/A	PCR	MS	Disease risk	There was a significant difference in RAGE 374 T/A genotype distribution between the controls and the MS patients.	The receptor for advanced glycation end products (RAGE) is a member of immunoglobulin superfamily of cell surface molecules.	19757202	Details
CYP24A1	SNP	rs4809960	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
CTLA4	SNP	TATG	PCR	MS	Disease risk	List of observed haplotypes among patients and healthy controls and the statistical analyses are summarized in Table 3.	Following surface expression, CTLA4 is reported to suppress T cell function by inducing indoleamine 2,13-dioxygenase metabolism in dendritic cells.	19737153	Details
OGG1	genotype	Ser/Ser	PCR	MS	Disease risk	Associations between genotype frequencies of GSTP1, OGG1 and XRCC1 gene polymorphisms and the risk of Multiple Sclerosis (MS).	Since polymorphisms in DNA repair genes can result in reduced DNA repair capacity	26562193	Details
TLR3	polymorphism	TLR9-1486	PCR	MS	Disease risk	There was no significant difference in genotypes and allele distribution of TLR9-1486 polymorphism between the MS patients and the controls.	N/A	20197609	Details
NR3C1	SNP	rs41423247	PCR	MS	Disease risk	We demonstrated significant differences in distribution of genotype, allele and haplotype frequencies of rs6189, rs41423247 and rs55829690 between the study groups	the long non-coding RNA (lncRNA) growth arrest specific 5 (GAS7) interacts with GR through binding to the DNA-binding domain (DBD) region and reduces GR transcriptional activity	31724909	Details
TLR9	SNP	rs5743836	PCR	MS	Disease risk	Our results show no significant association with MS and no protective effect of T-1237C concerning age of onset, disease severity or disease subtype in MS patients	N/A	18208876	Details
CTLA4	Allele	NA	PCR	MS	Disease risk	The results showed that the CTLA4 dimorphism does not affect susceptibility to MS in ethnic Russians, be these stratified or not with regard to DRB1 alleles corresponding to serologic specificities DR1 to DR16.	The allele polymorphism results from single nucleotide substitution (A/G) in position +49 of exon 1 and leads to substitution Thr-->Ala in the leader peptide.	12173468	Details
HMGB	SNP	rs538493533	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
AGER	homozygote	AA	PCR	MS	Disease risk	The AA homozygote variants were detected in 8% of the patients with MS, as compared with 19% of healthy controls (OR=2.75; 95% CI=1.3195.733, p=0.007).	The receptor for advanced glycation end products (RAGE) is a member of immunoglobulin superfamily of cell surface molecules.	19757202	Details
CYP24A1	SNP	rs6022999	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
CTLA4	SNP	TGCG	PCR	MS	Disease risk	List of observed haplotypes among patients and healthy controls and the statistical analyses are summarized in Table 3.	Following surface expression, CTLA4 is reported to suppress T cell function by inducing indoleamine 2,14-dioxygenase metabolism in dendritic cells.	19737153	Details
OGG1	genotype	Ser/Cys	PCR	MS	Disease risk	OGG1 Ser/Cys and Ser/Cys + Cys/Cys genotypes had higher MS risk.	Since polymorphisms in DNA repair genes can result in reduced DNA repair capacity	26562193	Details
ERVW-1	CNV	N/A	PCR	MS	Disease risk	MSRV pol sequence copy number was significantly greater in MS patients than in normal individuals.	N/A	14704480	Details
TLR3	polymorphism	TLR9 2848	PCR	MS	Disease risk	There was higher TLR9 2848 A allele frequency in the MS patients than in the controls, and higher risk in MS patients with A allele than those without.	N/A	20197609	Details
GAS5	SNP	rs55829688	PCR	MS	Disease risk	We demonstrated significant differences in distribution of genotype, allele and haplotype frequencies of rs6189, rs41423247 and rs55829691 between the study groups	the long non-coding RNA (lncRNA) growth arrest specific 5 (GAS8) interacts with GR through binding to the DNA-binding domain (DBD) region and reduces GR transcriptional activity	31724909	Details
TRIOBP	SNP	rs201693690	PCR	MS	Disease risk	MS in southern China may have association with unique genetic variants,our data suggest TRIOBP as a potential novel risk gene.	Multiple sclerosis (MS) is an autoimmune and demyelinating disease.Genome-wide association studies have shown that MS is associated with many genetic variants in some human leucocyte antigen genes and other immune-related genes,however, those studies were mostly specific to Caucasian populations.	30140248	Details
ADAMTS14	Allele	NA	PCR	MS	Disease risk	These findings suggest a potentially important role for the ADAMTS14 gene in predisposition to MS.	N/A	15913795	Details
HMGB	SNP	rs577524260	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
AGER	genotype	-479 T/C	PCR	MS	Disease risk	No differences were observed between the MS patients and the controls, concerning the frequencies of the 479 T/C and G82S genotypes of the RAGE.	The receptor for advanced glycation end products (RAGE) is a member of immunoglobulin superfamily of cell surface molecules.	19757202	Details
CYP24A1	SNP	rs6097797	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
CTLA4	SNP	TGTG	PCR	MS	Disease risk	List of observed haplotypes among patients and healthy controls and the statistical analyses are summarized in Table 3.	Following surface expression, CTLA4 is reported to suppress T cell function by inducing indoleamine 2,15-dioxygenase metabolism in dendritic cells.	19737153	Details
OGG1	genotype	Cys/Cys	PCR	MS	Disease risk	OGG1 Ser/Cys and Ser/Cys + Cys/Cys genotypes had higher MS risk.	Since polymorphisms in DNA repair genes can result in reduced DNA repair capacity	26562193	Details
NFASC	SNP	rs12368653	PCR	MS	Disease risk	The results showed a significant increase in dephosphorylated NF expression in patients heterozygous (AG/AG; p<0.05) or homozygous (AA/AA; p<0.05) for both the rs12368653 and rs703842 risk SNP, when compared to patients with no copy of either SNP.	N/A	26785938	Details
FCGR2A	Allele	NA	PCR	MS	Disease risk	The results of the present study add the FcgammaRIIA gene to the gene networks which determine the severity of MS in southern Iran.	Receptors for the Fc fragment of IgG (FcgammaR) might induce inflammatory responses through linking the humoral and cellular immune responses by targeting immune complexes to effector cells.	18698123	Details
MBP	Allele	NA	PCR	MS	Disease risk	Our study thus indicate that there is an association between MS and a length polymorphism of the 5’ I end to the MBP gene in Danish MS patients.	The myelin basic protein (MBP) gene is a candidate locus for disease susceptibility in multiple sclerosis (MS).	8739431	Details
HMGB	SNP	rs182881863	PCR	MS	Disease risk	Our results identified significant associations as well as significant allele frequency differences in some of the studied single-nucleotide polymorphisms inclding rs4935356, rs3177928, and rs7197 from HLA-DRA gene, and rs12722489 and rs12722490 variants from IL2RA gene (p< 0.05).	N/A	33178870	Details
AGER	genotype	G82S	PCR	MS	Disease risk	No differences were observed between the MS patients and the controls, concerning the frequencies of the 479 T/C and G82S genotypes of the RAGE.	The receptor for advanced glycation end products (RAGE) is a member of immunoglobulin superfamily of cell surface molecules.	19757202	Details
CYP24A1	SNP	rs6097801	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
OGG1	genotype	Ser/Cys + Cys/Cys	PCR	MS	Disease risk	Associations between genotype frequencies of GSTP1, OGG1 and XRCC1 gene polymorphisms and the risk of Multiple Sclerosis (MS).	Since polymorphisms in DNA repair genes can result in reduced DNA repair capacity	26562193	Details
NFASC	SNP	rs703842	PCR	MS	Disease risk	The results showed a significant increase in dephosphorylated NF expression in patients heterozygous (AG/AG; p<0.05) or homozygous (AA/AA; p<0.05) for both the rs12368653 and rs703842 risk SNP, when compared to patients with no copy of either SNP.	N/A	26785938	Details
CXCL8	SNP	rs2227306	PCR	MS	Disease risk	We describe for the first time a role of SNP rs2227306 of IL-8 gene in regulating the expression and the activity of this inflammatory cytokine in MS.	The interleukin (IL)-8C>T rs2227306 single nucleotide polymorphism (SNP) regulates IL-8 activity in other clinical conditions; however, its role in MS has never been investigated.	36803228	Details
IL7	Allele	NA	PCR	MS	Disease risk	We conclude that the IL7 gene is very unlikely to influence the genetic susceptibility to MS in this population.	IL7 is a nonredundant cytokine, essential for T cell survival and development in humans.	17913246	Details
HLA-DRB1	polymorphism	DRB1*1506	PCR	MS	disease risk	Further molecular subtyping of HLA-DRB1*15 among the pa tients revealed two novel alleles, DRB1*1506 (20%) and DRB1*1508 (30%), along with the commonly reported DRB1*1501 (50%) for the first time in MS patients that were hitherto unidentified from other parts of India and world as well.	N/A	12651075	Details
CYP24A1	SNP	rs6127119	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
XRCC1	genotype	Arg/Arg	PCR	MS	Disease risk	Associations between genotype frequencies of GSTP1, OGG1 and XRCC1 gene polymorphisms and the risk of Multiple Sclerosis (MS).	Since polymorphisms in DNA repair genes can result in reduced DNA repair capacity	26562193	Details
PDLIM7	genotype	N/A	PCR	MS	Disease risk	We found a variety of LMP-1 sequences in both MS and controls, with no significant differences between the groups.	N/A	18184350	Details
LINGO1	SNP	rs11856808	PCR	MS	Disease risk	These results suggest that LINGO1 rs9652490 and rs11856808 polymorphisms are not related with risk for MS. This study adds to other published evidence indicating that, to date, the LINGO1 SNPs studied here could be useful risk biomarkers of developing essential tremor, but not other movement disorders.	N/A	23574883	Details
BDNF	SNP	rs6265	PCR	MS	Treatment risk	BDNF Val66Met was associated with walking function improvement after rehabilitation in progressive MS patients.	Rehabilitation is fundamental for progressive multiple sclerosis (MS), but predictive biomarkers of motor recovery are lacking, making patient selection difficult.	35265024	Details
TRBV20OR9-2	Allele	NA	PCR	MS	Disease risk	The clonal nature of this rearrangement proved by PAGE and sequencing analysis may suggest an antigen- driven expansion of 76T cells and argues for a significant role of 7~ T-cells with V65-J61 rearrangement in MS pathogenesis.	T-cell receptor (TCR) 6 gene repertoire, as assessed by V~-J6 re- arrangements, has been analyzed in nine multiple sclerosis (MS) cases and in 30 healthy individuals by seminested PCR technique.	9138431	Details
HLA-DRB1	polymorphism	DRB1*1507	PCR	MS	disease risk	Further molecular subtyping of HLA-DRB1*15 among the pa tients revealed two novel alleles, DRB1*1506 (20%) and DRB1*1508 (30%), along with the commonly reported DRB1*1501 (50%) for the first time in MS patients that were hitherto unidentified from other parts of India and world as well.	N/A	12651075	Details
CYP24A1	SNP	rs912505	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
PLA2G7	polymorphism	TT	PCR	MS	Phenotypic risk	These findings suggest that the PAF-AH gene missense mutation has no relation to either susceptibility or severity of C-MS, yet its activity is down-regulated, and that the mutation has no relation with susceptibility of OS-MS, yet it may confer the severity of female OS-MS.	Such a decrease of PAF-AH activity may in part be responsible for the reported increase of PAF in MS plasma and CSF, and therefore could contribute to the inflammation and vascular permeability changes in the CNS of MS.	15081260	Details
XRCC1	genotype	Arg/Gln	PCR	MS	Disease risk	Associations between genotype frequencies of GSTP1, OGG1 and XRCC1 gene polymorphisms and the risk of Multiple Sclerosis (MS).	Since polymorphisms in DNA repair genes can result in reduced DNA repair capacity	26562193	Details
LINGO1	SNP	rs9652490	PCR	MS	Disease risk	These results suggest that LINGO1 rs9652490 and rs11856808 polymorphisms are not related with risk for MS. This study adds to other published evidence indicating that, to date, the LINGO1 SNPs studied here could be useful risk biomarkers of developing essential tremor, but not other movement disorders.	N/A	23574883	Details
IL23A	SNP	rs11209026	PCR	MS	Disease risk	These results indicated higher levels of IL-17 in MS patients that may be influenced by disease patterns, medication and gender. No association was observed between investigated SNPs and MS.	Interleukin (IL)-17/IL-23 axis performs a prominent role in the pathogenesis of several autoimmune disorders.	28717429	Details
TRBV20OR9-2	Allele	NA	PCR	MS	Disease risk	These results support the involvement of the TCRB region in MS susceptibility and encourage further study of the variable gene segments in this region	This study focused on susceptibility to MS within the b-chain of the T-cell antigen receptor (TCRB locus, 7q35) in a cohort of 122 RR-MS patients compared with 96 normal individuals using biallelic polymorphisms across the bv8s1(Vb8.1) to bv11s1 (Vb11) TCRB subregion.	10871824	Details
HLA-DRB1	polymorphism	DRB1*1508	PCR	MS	disease risk	Further molecular subtyping of HLA-DRB1*15 among the pa tients revealed two novel alleles, DRB1*1506 (20%) and DRB1*1508 (30%), along with the commonly reported DRB1*1501 (50%) for the first time in MS patients that were hitherto unidentified from other parts of India and world as well.	N/A	12651075	Details
CYP24A1	SNP	rs927650	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
PLA2G7	polymorphism	GT	PCR	MS	Phenotypic risk	These findings suggest that the PAF-AH gene missense mutation has no relation to either susceptibility or severity of C-MS, yet its activity is down-regulated, and that the mutation has no relation with susceptibility of OS-MS, yet it may confer the severity of female OS-MS.	Such a decrease of PAF-AH activity may in part be responsible for the reported increase of PAF in MS plasma and CSF, and therefore could contribute to the inflammation and vascular permeability changes in the CNS of MS.	15081260	Details
XRCC1	genotype	Gln/Gln	PCR	MS	Disease risk	Associations between genotype frequencies of GSTP1, OGG1 and XRCC1 gene polymorphisms and the risk of Multiple Sclerosis (MS).	Since polymorphisms in DNA repair genes can result in reduced DNA repair capacity	26562193	Details
HLA-DRB1	allele	HLA-DRB1*15:01	PCR	MS	Disease risk	Analysis of gray matter lesion size revealed a significant increase of cortical lesion size in cases with high HLA-DRB1 expression.	Our data indicate that increased HLA-DRB1 and -DRB5 expression in the brain ofpatients with MS may be an important factor in how the HLA-DR15 haplotype contributes to MS pathomechanisms in the target organ.	31882398	Details
IL23A	SNP	rs1004819	PCR	MS	Disease risk	These results indicated higher levels of IL-17 in MS patients that may be influenced by disease patterns, medication and gender. No association was observed between investigated SNPs and MS.	Interleukin (IL)-17/IL-23 axis performs a prominent role in the pathogenesis of several autoimmune disorders.	28717429	Details
IL-1B	Allele	NA	PCR	MS	Disease risk	Polymorphisms of the IL-1B genes and common alleles of IL-1RA were not considered as risk factors for MS disease. However, genotype TT at IL-1A (-889) location and the rare allele of IL-1RA3 can be a potential risk factor for the disease. Furthermore, inappropriate dieting behaviors and consumption of fast-food can increase the risk of MS.	Cytokines as important mediators have a critical role in appropriate immune responses, the irregular production of which can lead to Multiple Sclerosis (MS). Proinflammatory cytokine interleukin-1 (IL-1) triggers inflammatory responses. Function and production of the cytokine are influenced by IL-1 coding gene polymorphism and those antagonists gene polymorphism.	32148206	Details
HLA-A	polymorphism	HLA-A11	PCR	MS	disease risk	The study revealed a significant increase of HLA-A11, B16, Cw7, and DRB1*15.	N/A	12651075	Details
APOE	genotype	rs405509 [ 219 G/T]	PCR	MS	Phenotype risk	In this MS study, neither APOE allele status nor promoter region heterogeneity at positions β219 G/T or 113 C/G influenced the clinical disease severity, cognition, or cerebral atrophy.	N/A	19786693	Details
CYP24A1	SNP	rs3787555	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
PLA2G7	polymorphism	GG	PCR	MS	Phenotypic risk	These findings suggest that the PAF-AH gene missense mutation has no relation to either susceptibility or severity of C-MS, yet its activity is down-regulated, and that the mutation has no relation with susceptibility of OS-MS, yet it may confer the severity of female OS-MS.	Such a decrease of PAF-AH activity may in part be responsible for the reported increase of PAF in MS plasma and CSF, and therefore could contribute to the inflammation and vascular permeability changes in the CNS of MS.	15081260	Details
XRCC1	genotype	Arg/Gln + Gln/Gln	PCR	MS	Disease risk	XRCC1 Arg/Gln +Gln/Gln genotype increased the risk of MS.	Since polymorphisms in DNA repair genes can result in reduced DNA repair capacity	26562193	Details
IGHV4-39	Deletion	IGHV4-39	PCR	MS	Disease risk	We observed no significant differences in the observed deletion frequencies between MS cases and controls, or between benign and malignant cases. IGHV4-39 was not present in sequences of PCR products generated with Msdel1 from genomic DNA of individuals suspected to be carrying a homozygous deletion, based on previous screening at markers Msdel2-4.	Several studies have shown that immunoglobulin heavy chain variable (IGHV) gene segment usage in B cell populations of MS brain lesions and CSF is biased toward IGHV family 4 genes, in particular, gene IGHV4-39. Adding to the complexity of the locus, insertion–deletion polymorphisms contribute to haplotype variation.	20471699	Details
IL4	SNP	VNTR and +33 C/T	PCR	MS	Disease risk	We did not identify IL-4–IL4-R gene–gene interaction in determining susceptibility or clinical parameters of MS. Disease or genetic heterogeneity or both may be responsible for the observed lack of reproduction in different populations. Our data reinforce recent findings for a role of IL4-R in susceptibility to MS	genetic heterogeneity	16313303	Details
STAT4	Allele	NA	PCR	MS	Disease risk	STAT4 polymorphism was significantly associated with MS and JO-SLE. Though homozygous JO-SLE patients are more risky for severe disease manifestations, homozygous MS patients are not risky for severe disease disability.	Multiple sclerosis (MS) and systemic lupus erythematosus (SLE) are chronic autoimmune mediated diseases with strong genetic and environmental components.	29881250	Details
IL1RN	Allele	NA	PCR	MS	Disease risk	Polymorphisms of the IL-1B genes and common alleles of IL-1RA were not considered as risk factors for MS disease. However, genotype TT at IL-1A (-889) location and the rare allele of IL-1RA3 can be a potential risk factor for the disease. Furthermore, inappropriate dieting behaviors and consumption of fast-food can increase the risk of MS.	Cytokines as important mediators have a critical role in appropriate immune responses, the irregular production of which can lead to Multiple Sclerosis (MS). Proinflammatory cytokine interleukin-1 (IL-1) triggers inflammatory responses. Function and production of the cytokine are influenced by IL-1 coding gene polymorphism and those antagonists gene polymorphism.	32148206	Details
HLA-C	polymorphism	HLA-A12	PCR	MS	disease risk	The study revealed a significant increase of HLA-A11, B16, Cw7, and DRB1*15.	N/A	12651075	Details
APOE	genotype	rs440446 [113 C/G]	PCR	MS	Phenotype risk	In this MS study, neither APOE allele status nor promoter region heterogeneity at positions β219 G/T or 113 C/G influenced the clinical disease severity, cognition, or cerebral atrophy.	N/A	19786693	Details
CYP24A1	SNP	rs2244719	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
HLA-DPB1	polymorphisms	DPB10501	PCR	MS	Phenotypic risk	MS with DPB10501 showed severe optic neuritis, myelitis and CSF pleocytosis	N/A	17125797	Details
IL4	SNP	Q551*R	PCR	MS	Disease risk	We did not identify IL-4–IL4-R gene–gene interaction in determining susceptibility or clinical parameters of MS. Disease or genetic heterogeneity or both may be responsible for the observed lack of reproduction in different populations. Our data reinforce recent findings for a role of IL4-R in susceptibility to MS	genetic heterogeneity	16313303	Details
TNFRSF1A	SNP	rs4149584	PCR	MS	Disease risk	Variant rs4149584 is associated with risk of developing MS. We analyzed its functional role in oligodendrocyte lineage cells and found an association with MS in homozygous carriers.	Genomic studies have identified numerous genetic variants associated with susceptibility to multiple sclerosis (MS); however, each one explains only a small percentage of the risk of developing the disease.	35963536	Details
HLA-DRB1	Allele	NA	PCR	MS	Disease risk	A very strong correlation of demielinating disease with DRB1*150 ... alleles was verified.	Using PCR-SSP technique genomic typing was performed on HLA DRB1 gene (chromosome 6p21) of 56 unrelated children with ON registered at least once in clinically verified MS.	12506649	Details
HLA-B	polymorphism	HLA-A13	PCR	MS	disease risk	The study revealed a significant increase of HLA-A11, B16, Cw7, and DRB1*15.	N/A	12651075	Details
APOE	genotype	rs440446 [113 C/C]	PCR	MS	Phenotype risk	In this MS study, neither APOE allele status nor promoter region heterogeneity at positions β219 G/T or 113 C/G influenced the clinical disease severity, cognition, or cerebral atrophy.	N/A	19786693	Details
CYP24A1	SNP	rs2296241	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
HLA-DQA1	polymorphism	DQAl*0102	PCR	MS	Disease risk	In French Canadians, MS was positively associated with DQAl"0102 and DQB1*0602, but there was no positive association of either allele with Sardinian MS, which, by contrast, was positively associated with DQB1*0302 and *0201 and with DQA1*0301, whereas none of these alleles was MS-associated in French Canadians.	N/A	8450999	Details
TAP1	allele	Ile	PCR	MS	Disease risk	Our results do not support a role for the five polymorphisms examined in the etiology of this disease.	N/A	7797617	Details
PDCD1	intronic polymorphism	7146G/A	PCR	MS	Disease risk	Importantly, PD-1–mediated inhibition of T-cell cytokine secretion (interferon-) is impaired in patients carrying the PD-1 polymorphism. In conclusion, our data suggest that PD-1 polymorphism is a genetic modifier of the progression of MS, possibly through inducing a partial defect in PD-1–mediated inhibition of T-cell activation.	a genetic modifier of the progression of MS	15912506	Details
AQP4	SNP	NA	PCR	MS	Disease risk	Statistical analyses showed no significant associations between AQP4 SNPs/haplotypes and development of IDD, including MS and NMO (P>0.05). Further replications in larger cohorts and other ethnic groups are needed.	Multiple sclerosis (MS) and neuromyelitis optica (NMO) are demyelinating autoimmune inflammatory diseases that affect the central nervous system (CNS). Previous genome-wide or candidate gene studies have suggested that genetic variants might be associated with the risk of MS or NMO.	24361961	Details
CHI3L1	SNP	rs4950928	PCR	MS	Disease risk	Allele C of rs4950928 was significantly associated with PPMS patients and with higher plasma CHI3L1 levels.	Chitinase 3-like 1 (CHI3L1) is upregulated in a wide variety of inflammatory conditions. Recent studies have pointed to a role of CHI3L1 in multiple sclerosis (MS) pathogenesis.	22183936	Details
ATXN2	polymorphism	the 22 repeat length allele	PCR	MS	phenotypics risk	However, transmission disequilibrium testing for these repeats demonstrated significant excess transmission of the 22 repeat length allele of the SCA2 gene (Pp4.4E 06) in multiple sclerosis patients.	N/A	10369884	Details
APOE	genotype	rs440446 [113 G/G]	PCR	MS	Phenotype risk	In this MS study, neither APOE allele status nor promoter region heterogeneity at positions β219 G/T or 113 C/G influenced the clinical disease severity, cognition, or cerebral atrophy.	N/A	19786693	Details
CYP24A1	SNP	rs2426496	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
HLA-DQB1	polymorphism	DQB1*0201	PCR	MS	Disease risk	In French Canadians, MS was positively associated with DQAl"0102 and DQB1*0602, but there was no positive association of either allele with Sardinian MS, which, by contrast, was positively associated with DQB1*0302 and *0201 and with DQA1*0301, whereas none of these alleles was MS-associated in French Canadians.	N/A	8450999	Details
TAP1	allele	Val	PCR	MS	Disease risk	Our results do not support a role for the five polymorphisms examined in the etiology of this disease.	N/A	7797617	Details
IL13	promoter polymorphism	IL-131024TT	PCR	MS	Disease risk	we demonstrated a strong association (P = 1.09E-05) between the IL-13 1024 marker and inhalation allergy. Furthermore, we showed for the first time that this association also exists in atopic dermatitis (P = 2.0E-02). No association with MS was found.	N/A	14641544	Details
CNR1	Allele	NA	PCR	MS	Treatment risk	Our results provide the first evidence that genetic differences within the CB1R may influence clinical responses to exercise therapy, and they strengthen the hypothesis that CB1Rs are involved in the regulation of synaptic plasticity and in the control of spasticity in humans.	Therapeutic effects of physical therapy in neurologic disorders mostly rely on the promotion of use-dependent synaptic plasticity in damaged neuronal circuits.	25520956	Details
GSTT1	Allele	NA	PCR	MS	Disease risk	The results suggest that GSTT1 and GSTM1 have no major pathogenetic role on the MS occurrence, nor any strong modifying effect on the disability status	Glutathione-S-transferases (GSTs) are detoxification enzymes, evolved to protect cells against reactive oxygen metabolites.	17437619	Details
APOE	polymorphism	e2	PCR	MS	phenotypics risk	The e2 allele was associated with increased time to moderate disability.	N/A	21325856	Details
APOE	genotype	rs405509 [ 219 G/G]	PCR	MS	Phenotype risk	In this MS study, neither APOE allele status nor promoter region heterogeneity at positions β219 G/T or 113 C/G influenced the clinical disease severity, cognition, or cerebral atrophy.	N/A	19786693	Details
CYP24A1	SNP	rs2585428	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
HLA-DQB1	polymorphism	DQBl*O302	PCR	MS	Disease risk	In French Canadians, MS was positively associated with DQAl"0102 and DQB1*0602, but there was no positive association of either allele with Sardinian MS, which, by contrast, was positively associated with DQB1*0302 and *0201 and with DQA1*0301, whereas none of these alleles was MS-associated in French Canadians.	N/A	8450999	Details
TAP1	allele	Asp	PCR	MS	Disease risk	Our results do not support a role for the five polymorphisms examined in the etiology of this disease.	N/A	7797617	Details
HLA-DRB1	allele	HLA-DRB1*15:01	PCR	MS	Disease risk	with a homogenous distribution across the country. HLA-DRB1*15 is a relevant MS susceptibility locus in the Italian population, possibly with little influence on the occurrence of concomitant autoimmune disorders.	HLA-DRB1*15 is a relevant MS susceptibility locus in the Italian population	23279712	Details
CD14	Allele	NA	PCR	MS	Disease risk	In summary, we conclude that CD14-159 and -260 polymorphisms are associated with the risk of MS in Iranian population and affects CD14 promoter activity, thereby regulating CD14 expression.	Besides the central role of the adaptive immune system, a disturbance of innate immune system is also suggested to be involved in the pathogenesis of multiple sclerosis (MS).	27819517	Details
GSTM1	Allele	NA	PCR	MS	Disease risk	The results suggest that GSTT1 and GSTM1 have no major pathogenetic role on the MS occurrence, nor any strong modifying effect on the disability status	Glutathione-S-transferases (GSTs) are detoxification enzymes, evolved to protect cells against reactive oxygen metabolites.	17437619	Details
LIF	SNP	SNP3951	PCR	MS	disease risk	In summary, no association was found between the studied LIF DNA polymorphisms and the prevalence of MS indicating that these polymorphisms are not involved in determining disease susceptibility.	Indeed, these polymorphisms might have an impact on the neuroprotective effects of LIF, thus compromising tissue repair and disease recovery.	16263181	Details
APOE	genotype	rs405509 [ 219 T/T]	PCR	MS	Phenotype risk	In this MS study, neither APOE allele status nor promoter region heterogeneity at positions β219 G/T or 113 C/G influenced the clinical disease severity, cognition, or cerebral atrophy.	N/A	19786693	Details
DBP	SNP	rs7041	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
HLA-DQB1	polymorphism	DQBl*0602	PCR	MS	Disease risk	In French Canadians, MS was positively associated with DQAl"0102 and DQB1*0602, but there was no positive association of either allele with Sardinian MS, which, by contrast, was positively associated with DQB1*0302 and *0201 and with DQA1*0301, whereas none of these alleles was MS-associated in French Canadians.	N/A	8450999	Details
TAP1	allele	Gly	PCR	MS	Disease risk	Our results do not support a role for the five polymorphisms examined in the etiology of this disease.	N/A	7797617	Details
IL18	Allele	NA	PCR	MS	Disease risk	In this study, we showed the significant higher IL-18 serum level and significant different frequencies of two polymorphisms of IL-18 in MS patients. These results show the important roles of IL-18 in MS pathogenesis. However, more studies are needed to verify our results in larger sample size.	Multiple sclerosis (MS) is a chronic demyelinating disorder of central nervous system. Although the definite pathogenesis of MS has not been understood, crucial role of environmental and genetic risk factors has been proposed.	31736573	Details
CD24	Allele	NA	PCR	MS	Disease risk	Our results demonstrate that a destabilizing dinucleotide deletion in the 39 UTR of CD24 mRNA conveys significant protection against both MS and SLE.	We used cases/control studies to determine the association between CD24 polymorphism and the risk of MS and SLE.	17411341	Details
MMP9	SNP	rs6073751	PCR	MS	Disease risk	In conclusion, our results do not suggest that MS susceptibility is affected by known genetic variants within MMP9, although MMP9 itself may play an important role in MS pathophysiology	Our aims were (a) to improve the statistical power by genotyping a large sample size, (b) to nominally increase the SNP coverage of the MMP9 region and the flanking +/2 mega base pairs (Mbp), a region containing more than 70 genes, by imputation of additional variants, and (c) to perform a meta-analysis on our own findings together with published data	25670000	Details
LIF	SNP	SNP2680	PCR	MS	disease risk	In summary, no association was found between the studied LIF DNA polymorphisms and the prevalence of MS indicating that these polymorphisms are not involved in determining disease susceptibility.	Indeed, these polymorphisms might have an impact on the neuroprotective effects of LIF, thus compromising tissue repair and disease recovery.	16263181	Details
MMP3	polymorphisms	5A/6A	PCR	MS	Disease risk	Results show that the distribution of MMP-3 5A/6A genotype frequencies between MS patients and controls were not significantly different.	MMP-3 cleaves human myelin basic protein (MBP).	17942123	Details
DBP	SNP	rs705120	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
HLA-DQB1	polymorphism	DQB1*0301	PCR	MS	Disease risk	In French Canadians, MS was positively associated with DQAl"0102 and DQB1*0602, but there was no positive association of either allele with Sardinian MS, which, by contrast, was positively associated with DQB1*0302 and *0201 and with DQA1*0301, whereas none of these alleles was MS-associated in French Canadians.	N/A	8450999	Details
TAP1	genotype	Ile/Ile	PCR	MS	Disease risk	Our results do not support a role for the five polymorphisms examined in the etiology of this disease.	N/A	7797617	Details
TYK2	SNP	rs34536443	PCR	MS	Disease risk	by mega-analysis of 10642 MS patients, 10620 controls and 2110 MS trios, the association at genome-wide significance level (P录5.08 10 9, OR 0.77) was shown.	protective	19888296	Details
IL-27	snp	rs 153109	PCR	MS	Disease risk	The results of the current study showed a significant relationship of IL-27-A964G and IL-27-T4730C polymorphisms with increased risk of MS, and also the protective role of the IL-23-R381Q polymorphism. Moreover, the haplotype-based analysis proposed the mutant G-C (A924G, T4730C) as a significant risk haplotype for the development of MS.	Background: interleukin 23 (IL-23) and interleukin 27 (IL-27) modulate the activity of T helper 17 cells (Th17) with critical roles in autoimmune diseases and multiple sclerosis (MS).	35011777	Details
HLA-DRB1	Allele	NA	PCR	MS	Disease risk	Cross-ethnic comparison between the two HLA haplotypes associated with MS in Sardi-nians and the DRB1*1501 (DR2)–DQA1*0102–DQB1*0602 haplotype, associated with MS in other Caucasian populations, failed to identify any shared epitopes in the DR and DQ molecules that segregated with disease sus-ceptibility.	Previous genetic analyses have suggested that the MHC/HLA region on chromosome 6p21 contains an MS-predisposing component.	9668164	Details
MMP9	SNP	rs3918242	PCR	MS	Disease risk	In conclusion, our results do not suggest that MS susceptibility is affected by known genetic variants within MMP9, although MMP9 itself may play an important role in MS pathophysiology	Our aims were (a) to improve the statistical power by genotyping a large sample size, (b) to nominally increase the SNP coverage of the MMP9 region and the flanking +/2 mega base pairs (Mbp), a region containing more than 70 genes, by imputation of additional variants, and (c) to perform a meta-analysis on our own findings together with published data	25670000	Details
Eae16	N/A	N/A	PCR	EAE	phenotypics risk	Eae16 and Eae17 differ from those found in previously studied strain combinations, thus demonstrating genetic heterogeneity of EAE.	Eae16 belongs to this category, as it displayed asso ciation with disease severity and duration, but not incidence.	12517974	Details
DBP	SNP	rs4588	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
HLA-DQA1	polymorphism	DQAl*0102	PCR	MS	Disease risk	In French Canadians, MS was positively associated with DQAl"0102 and DQB1*0602, but there was no positive association of either allele with Sardinian MS, which, by contrast, was positively associated with DQB1*0302 and *0201 and with DQA1*0301, whereas none of these alleles was MS-associated in French Canadians.	N/A	8450999	Details
TAP1	genotype	Ile/Val	PCR	MS	Disease risk	Our results do not support a role for the five polymorphisms examined in the etiology of this disease.	N/A	7797617	Details
IL-27	snp	rs 181206	PCR	MS	Disease risk	The results of the current study showed a significant relationship of IL-27-A964G and IL-27-T4730C polymorphisms with increased risk of MS, and also the protective role of the IL-23-R381Q polymorphism. Moreover, the haplotype-based analysis proposed the mutant G-C (A924G, T4730C) as a significant risk haplotype for the development of MS.	Background: interleukin 23 (IL-23) and interleukin 27 (IL-27) modulate the activity of T helper 17 cells (Th17) with critical roles in autoimmune diseases and multiple sclerosis (MS).	35011777	Details
HLA-DQA1	Allele	NA	PCR	MS	Disease risk	Cross-ethnic comparison between the two HLA haplotypes associated with MS in Sardi-nians and the DRB1*1501 (DR2)–DQA1*0102–DQB1*0602 haplotype, associated with MS in other Caucasian populations, failed to identify any shared epitopes in the DR and DQ molecules that segregated with disease sus-ceptibility.	Previous genetic analyses have suggested that the MHC/HLA region on chromosome 6p21 contains an MS-predisposing component.	9668164	Details
Eae17	N/A	N/A	PCR	EAE	phenotypics risk	Eae16 and Eae17 differ from those found in previously studied strain combinations, thus demonstrating genetic heterogeneity of EAE.	Thus, this locus could interact and/or be activated as a disease promoting locus, dependent on the origin of the animal.	12517974	Details
GC	SNP	rs7041	PCR	MS	Disease risk	We did not observe any statically significant difference in the distribution of genotypic VDBP variants between the study groups.	VDBP has a role in immune system as a chemotactic factor for neutrophil leucocytes and osteoclast activation.	27904983	Details
DBP	SNP	rs2282679	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
HLA-DQB1	polymorphism	DQBl*0602	PCR	MS	Disease risk	In French Canadians, MS was positively associated with DQAl"0102 and DQB1*0602, but there was no positive association of either allele with Sardinian MS, which, by contrast, was positively associated with DQB1*0302 and *0201 and with DQA1*0301, whereas none of these alleles was MS-associated in French Canadians.	N/A	8450999	Details
TAP1	genotype	Val/Val	PCR	MS	Disease risk	Our results do not support a role for the five polymorphisms examined in the etiology of this disease.	N/A	7797617	Details
IL23A	Allele	NA	PCR	MS	Disease risk	The results of the current study showed a significant relationship of IL-27-A964G and IL-27-T4730C polymorphisms with increased risk of MS, and also the protective role of the IL-23-R381Q polymorphism. Moreover, the haplotype-based analysis proposed the mutant G-C (A924G, T4730C) as a significant risk haplotype for the development of MS.	Background: interleukin 23 (IL-23) and interleukin 27 (IL-27) modulate the activity of T helper 17 cells (Th17) with critical roles in autoimmune diseases and multiple sclerosis (MS).	35011777	Details
HLA-DQB1	Allele	NA	PCR	MS	Disease risk	Cross-ethnic comparison between the two HLA haplotypes associated with MS in Sardi-nians and the DRB1*1501 (DR2)–DQA1*0102–DQB1*0602 haplotype, associated with MS in other Caucasian populations, failed to identify any shared epitopes in the DR and DQ molecules that segregated with disease sus-ceptibility.	Previous genetic analyses have suggested that the MHC/HLA region on chromosome 6p21 contains an MS-predisposing component.	9668164	Details
TNFRSF1A	polymorphism	exon1	PCR	MS	disease risk	No significant differences were observed for both polymorphisms between the patients and the controls.	N/A	11598334	Details
GC	SNP	rs4588	PCR	MS	Disease risk	We did not observe any statically significant difference in the distribution of genotypic VDBP variants between the study groups.	VDBP has a role in immune system as a chemotactic factor for neutrophil leucocytes and osteoclast activation.	27904983	Details
DBP	SNP	rs2298850	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
TAP2	allele	Ile	PCR	MS	Disease risk	Our results do not support a role for the five polymorphisms examined in the etiology of this disease.	N/A	7797617	Details
TNF	SNP	(rs1799964	PCR	MS	Disease risk	Examining the effect of each SNP in the presence or absence of the HLA DRB1*1501 risk allele identified significant associations with TNF α -1031 (rs1799964) among those without the HLA risk allele.	DNA was available from 722 individuals (223 with MS and 499 controls) who participated in a population-based case-control study.	25741530	Details
NOS2A	Allele	NA	PCR	MS	Disease risk	The very largest study of NOS2A variation in MS, to date, excludes even a modest role for this locus in susceptibility.	Variation in the major histocompatibility complex (MHC) on chromosome 6p21, specifically the HLA-DRB1*15 haplotype, is the strongest genetic factor for MS, yet it is estimated to account for only a portion of risk for the disease.	18580885	Details
TLR7	polymorphism	intron 6	PCR	MS	disease risk	No significant differences were observed for both poly morphisms between the patients and the controls.	N/A	11598334	Details
CYP27B1	SNP	rs118204009	PCR	MS	Disease risk	We did not observe any case of all three CYP27B1 variants among MS patients as well as controls.	1,25(OH)2D, the biologically active metabolite, is the result of a second hydroxylation in the kidney, catalyzed by the 1 a hydroxylase, CYP27B1.	27904983	Details
DBP	SNP	rs1352845	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
APOA1	allel	A	PCR	MS	Phenotypic risk	APOA1 A-allele carriers displayed superior overall cognitive performance compared with non-carriers (P 0.008) and had a three-fold decrease in the relative risk of overall cognitive impairment.	With decreased reverse cholesterol transport from brain to periphery possibly leading to cerebral cholesterol accumulation favoring amyloidogenesis, elevated ApoA1 levels may act in a protective fashion.	18805838	Details
TAP2	allele	Val	PCR	MS	Disease risk	Our results do not support a role for the five polymorphisms examined in the etiology of this disease.	N/A	7797617	Details
HLA-DRB1	Allele	NA	PCR	MS	Disease risk	Examining the effect of each SNP in the presence or absence of the HLA DRB1*1501 risk allele identified significant associations with TNF α -1031 (rs1799964) among those without the HLA risk allele.	DNA was available from 722 individuals (223 with MS and 499 controls) who participated in a population-based case-control study.	25741530	Details
OAS1	Allele	NA	PCR	MS	Disease risk	A functional OAS1 SNP, AA genotype, confers susceptibility to MS and the GG genotype may protect against increased disease activity.	A single nucleotide polymorphism (SNP) in exon 7 of OAS1 results in differential RNAseL enzyme activity, the A allele coding for a truncated form with low activity and the G conferring high activity.	20679634	Details
CCL5	polymorphism	RANTES-403G/A	PCR	MS	disease risk	MS cases differed from controls showing a significant association with the 403G/A polymorphism.	N/A	15471370	Details
CYP27B1	SNP	rs118204011	PCR	MS	Disease risk	We did not observe any case of all three CYP27B1 variants among MS patients as well as controls.	1,25(OH)2D, the biologically active metabolite, is the result of a second hydroxylation in the kidney, catalyzed by the 1 a hydroxylase, CYP27B1.	27904983	Details
DBP	SNP	rs12512631	PCR	MS	Disease risk	We found no significant association of vitamin D pathway genes with MS susceptibility after correction for multiple comparisons.	N/A	21440908	Details
APOA1	polymorphisms	APOA1 –75G/A	PCR	MS	Phenotypic risk	We found an association of the APOA1 –75G/A promoter polymorphism with cognitive performance in MS.	The APOA1 –75 G/A promoter polymorphism could exert the observed effect on cognition through a direct influence on ApoA1 levels.	18805838	Details
TAP2	allele	Asp	PCR	MS	Disease risk	Our results do not support a role for the five polymorphisms examined in the etiology of this disease.	N/A	7797617	Details
HLA-A	SNP	rs9267649	PCR	MS	Disease risk	The present research results provide further evidence on the association of the two variants rs9267649 of the HLA and rs2248359 of the CYP24A1 gene with MS etiology and an increased risk of MS in Iranian RRMS patients.	Studies have shown that MS results from synergism between genetic and environmental factors.	36381285	Details
MBP	SNP	rs12959006	PCR	MS	Disease risk	Our study, and those from others, consolidates the contribution of rs12959006, within the MBP gene, as a marker to predict MS activity. Furthermore, according to our results, there seems to be an influence of both the genetic polymorphism in MBP and HHV-6 infection in predicting a higher relapse rate that is exclusive to male MS patients	MBP is part of the peptide cocktail used for inducing experimental autoimmune encephalomyelitis (EAE) in mice, along with proteolipid protein (PLP) and myelin olygodendrocyte glycoprotein (MOG)	32431704	Details
CCL5	polymorphism	RANTES-28G	PCR	MS	phenotypics risk	There was a significant association of the -28G allele with both early onset and longer survival.	N/A	15471370	Details
CYP27B1	SNP	rs118204012	PCR	MS	Disease risk	We did not observe any case of all three CYP27B1 variants among MS patients as well as controls.	1,25(OH)2D, the biologically active metabolite, is the result of a second hydroxylation in the kidney, catalyzed by the 1 a hydroxylase, CYP27B1.	27904983	Details
Cia2	Chromosome	1	PCR	EAE	Disease risk	Linkage between previously described arthritis QTL and MOG-induced EAE disease phenotypes	Quantitative trait loci (QTL) controlling inflammatory diseases	9692888	Details
TAP2	allele	Gly	PCR	MS	Disease risk	Our results do not support a role for the five polymorphisms examined in the etiology of this disease.	N/A	7797617	Details
IL17A	SNP	rs2275913	PCR	MS	Disease risk	Concerning the distribution of allele and genotype, the A/G allele of SNP rs2275913 was not related to MS.	Multiple sclerosis (MS) is autoimmune demyelinating diseases of the central nervous system with complex pathogenesis.IL-17A has been shown to play an important role in the pathogenesis of certain autoimmune diseases.	22118860	Details
CYP24A1	SNP	rs2248359	PCR	MS	Disease risk	The present research results provide further evidence on the association of the two variants rs9267649 of the HLA and rs2248359 of the CYP24A1 gene with MS etiology and an increased risk of MS in Iranian RRMS patients.	Studies have shown that MS results from synergism between genetic and environmental factors.	36381285	Details
CCL5	polymorphism	RANTES-28C/G	PCR	MS	disease risk	MS cases differed from controls showing a significant association with the 403G/A polymorphism,but not the -28C/G.	N/A	15471370	Details
GC	phenotype	Gc1S/Gc1S	PCR	MS	Disease risk	Moreover, the three major electrophoretic variants of the VDBP, Gc1f, Gc1s, and Gc2, did not differ between MS patients and control group	VDBP has a role in immune system as a chemotactic factor for neutrophil leucocytes and osteoclast activation.	27904983	Details
Cia3	Chromosome	4	PCR	EAE	Disease risk	We conclude that Cia3 and Oia2 regulate MOG-induced EAE in rats.	Quantitative trait loci (QTL) controlling inflammatory diseases	9692888	Details
NR3C1	polymorphisms	rs6195(AA)	PCR	MS	Phenotypic risk	None of the identified alleles/genotypes were found to be associated with the severity of disease, response to glucocorticoids and disease subtypes.	N/A	27000245	Details
TAP2	genotype	Ile/Ile	PCR	MS	Disease risk	Our results do not support a role for the five polymorphisms examined in the etiology of this disease.	N/A	7797617	Details
IL17F	SNP	rs763780	PCR	MS	Disease risk	The difference between C-MS and controls did not quite reach statistical significance.	Multiple sclerosis (MS) is autoimmune demyelinating diseases of the central nervous system with complex pathogenesis.IL-17F has been shown to play an important role in the pathogenesis of certain autoimmune diseases.	22118860	Details
VDR	Allele	NA	PCR	MS	Disease risk	These data seem to exclude a role of VDREs in the promoter region of the DRB1 gene in susceptibility to MS carried by DRB1* alleles in Sardinian patients.	Vitamin D response elements (VDREs) have been found in the promoter region of the MS-associated allele HLA-DRB1*15:01,suggesting that with low vitamin D availability VDREs are incapable of inducing *15:01 expression allowing in early life autoreactive T-cells to escape central thymic deletion.	22848563	Details
APOE	gene polymorphisms	N/A	PCR	MS	Disease risk	The results of present study are in agreement with the historical evidences which show admixture of Iranian population with other populations and some studies based on genetic polymorphisms in the population of Southern Iran	Apolipoprotein E (apoE) with three major alleles E2, E3 and E4 is one of the critical genes in lipid metabolism. Common apoE alleles are in association with an increase in risk for central nervous and cardiovascular diseases such as Alzheimer’s disease, dementia, multiple sclerosis, atherosclerosis, coronary heart disease, hyperlipoproteinemia and stroke	17594534	Details
TRB	polymorphism	TCRBV8	PCR	MS	disease risk	Although the HLA DR2 genotype was significantly associated with MS, no interactive effects were seen with MS, DR2, TCRAC1, TCRBC2 and TCRBV alleles.	N/A	7911477	Details
GC	phenotype	Gc1S/Gc2	PCR	MS	Disease risk	Moreover, the three major electrophoretic variants of the VDBP, Gc1f, Gc1s, and Gc2, did not differ between MS patients and control group	VDBP has a role in immune system as a chemotactic factor for neutrophil leucocytes and osteoclast activation.	27904983	Details
Cia2	Chromosome	4	PCR	EAE	Disease risk	We conclude that Cia3 and Oia2 regulate MOG-induced EAE in rats.	Quantitative trait loci (QTL) controlling inflammatory diseases	9692888	Details
TGFB1	polymorphism	N/A	PCR	MS	Disease risk	These data indicate that TGF-b1 and b2 genes are not loci inˉuencing MS susceptibility, either RR/SPMS or PPMS, in this population.	TGF-b is produced by activated T cells, B cells and macrophages	10335519	Details
NR3C1	polymorphisms	rs6195(AG)	PCR	MS	Phenotypic risk	None of the identified alleles/genotypes were found to be associated with the severity of disease, response to glucocorticoids and disease subtypes.	N/A	27000245	Details
TAP2	genotype	Ile/Val	PCR	MS	Disease risk	Our results do not support a role for the five polymorphisms examined in the etiology of this disease.	N/A	7797617	Details
MMP9	Allele	NA	PCR	MS	Disease risk	These results suggest that a genetic polymorphism of the MMP-9 promoter region may influence the susceptibility to MS	To investigate the role of the matrix metalloproteinase-9 gene (MMP-9) in multiple sclerosis (MS), we analyzed the functional and n repeat polymorphisms in 243 Italian patients with MS and 173 healthy controls.	20471697	Details
TOR1A	SNP	rs2395182,	PCR	MS	Disease risk	At first the sensitivity and specificity for DQ2.2 was high and accurate but the predictive value was low. The SNPs for DQ2.2 (rs2395182, rs7775228) not only tagged DQ2.2 but also included the relatively infrequent DQ4 allele. We therefore decided to tag DQ4 as well (rs4713586) making it possible to call a person DQ2.2 when the alleles were positive for DQ2.2 and negative for DQ4	The HLA genes, located in the MHC region on chromosome 6p21.3, play an important role in many autoimmune disorders, such as celiac disease (CD), type 1 diabetes (T1D), rheumatoid arthritis, multiple sclerosis, psoriasis and others. Known HLA variants that confer risk to CD, for example, include DQA1*05/DQB1*02 (DQ2.5) and DQA1*03/ DQB1*0302 (DQ8). To diagnose the majority of CD patients and to study disease susceptibility and progression, typing these strongly associated HLA risk factors is of utmost importance.	18509540	Details
TRB	polymorphism	TCRBV11	PCR	MS	disease risk	Although the HLA DR2 genotype was significantly associated with MS, no interactive effects were seen with MS, DR2, TCRAC1, TCRBC2 and TCRBV alleles.	N/A	7911477	Details
GC	phenotype	Gc1S/Gc1F	PCR	MS	Disease risk	Moreover, the three major electrophoretic variants of the VDBP, Gc1f, Gc1s, and Gc2, did not differ between MS patients and control group	VDBP has a role in immune system as a chemotactic factor for neutrophil leucocytes and osteoclast activation.	27904983	Details
Cia4	Chromosome	7	PCR	EAE	Disease risk	Linkage between previously described arthritis QTL and MOG-induced EAE disease phenotypes	Quantitative trait loci (QTL) controlling inflammatory diseases	9692888	Details
TGFB2	polymorphism	N/A	PCR	MS	Disease risk	These data indicate that TGF-b1 and b2 genes are not loci inˉuencing MS susceptibility, either RR/SPMS or PPMS, in this population.	TGF-b is produced by activated T cells, B cells and macrophages	10335519	Details
NR3C1	allel	rs6195(A)	PCR	MS	Phenotypic risk	None of the identified alleles/genotypes were found to be associated with the severity of disease, response to glucocorticoids and disease subtypes.	N/A	27000245	Details
TAP2	genotype	Val/Val	PCR	MS	Disease risk	Our results do not support a role for the five polymorphisms examined in the etiology of this disease.	N/A	7797617	Details
APOE	Alleles	NA	PCR	MS	Disease risk	ApoE ?4 patients (n=10) had a higher percent-age of partially recovered relapses (62%) as opposed to the non-?4 patients (n=26) who more commonly had completely rather than partially (42%) resolved relapses.	Although APOE does not seem to be implicated in the early patho- genesis of the disease, patients possessing the ?4 allele might have a reduced capacity for neuronal remodelling after relapses.	10406990	Details
HLA-DRB1	Allele	NA	PCR	MS	Disease risk	Among those with both genetic risk factors, smoking increased the risk by a factor of 2.8 in comparison with a factor of 1.4 among those without the genetic risk factors.	Both genetic and environmental factors display low or modest associations with multiple sclerosis. Hypothetically, gene–envir-onment interactions may exert much stronger effects. In this study, we investigated potential interactions between genetic risk factors and smoking in relation to risk of developing multiple sclerosis.	21303861	Details
TOR1A	SNP	rs7775228	PCR	MS	Disease risk	At first the sensitivity and specificity for DQ2.2 was high and accurate but the predictive value was low. The SNPs for DQ2.2 (rs2395182, rs7775228) not only tagged DQ2.2 but also included the relatively infrequent DQ4 allele. We therefore decided to tag DQ4 as well (rs4713586) making it possible to call a person DQ2.2 when the alleles were positive for DQ2.2 and negative for DQ4	The HLA genes, located in the MHC region on chromosome 6p21.3, play an important role in many autoimmune disorders, such as celiac disease (CD), type 1 diabetes (T1D), rheumatoid arthritis, multiple sclerosis, psoriasis and others. Known HLA variants that confer risk to CD, for example, include DQA1*05/DQB1*02 (DQ2.5) and DQA1*03/ DQB1*0302 (DQ8). To diagnose the majority of CD patients and to study disease susceptibility and progression, typing these strongly associated HLA risk factors is of utmost importance.	18509540	Details
TRB	polymorphism	TCRBC2	PCR	MS	disease risk	Although the HLA DR2 genotype was significantly associated with MS, no interactive effects were seen with MS, DR2, TCRAC1, TCRBC2 and TCRBV alleles.	N/A	7911477	Details
GC	phenotype	Gc1F/Gc2	PCR	MS	Disease risk	Moreover, the three major electrophoretic variants of the VDBP, Gc1f, Gc1s, and Gc2, did not differ between MS patients and control group	VDBP has a role in immune system as a chemotactic factor for neutrophil leucocytes and osteoclast activation.	27904983	Details
Cia3	Chromosome	10	PCR	EAE	Disease risk	Linkage between previously described arthritis QTL and MOG-induced EAE disease phenotypes	Quantitative trait loci (QTL) controlling inflammatory diseases	9692888	Details
HLA-DQA1	polymorphism	DQA1*0101	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
NR3C1	allel	rs6195(G)	PCR	MS	Phenotypic risk	None of the identified alleles/genotypes were found to be associated with the severity of disease, response to glucocorticoids and disease subtypes.	N/A	27000245	Details
MPO	SNP	NA	PCR	MS	Disease risk	In this study, we investigated two polymorphisms located in the promotor region of the MPO gene, known to influence the expression of MPO, in a large case/control material consisting of 871 Swedish MS patients and 532 Swedish healthy controls.	MPO is an enzyme found in myeloid cells which catalyses the production of hypochlorus acid, a potent microbicidal agent. It also plays an important role in inflammatory processes, where migrating neutrophiles may release active MPO and cause tissue damage.	17613595	Details
HLA-A	Allele	NA	PCR	MS	Disease risk	Among those with both genetic risk factors, smoking increased the risk by a factor of 2.8 in comparison with a factor of 1.4 among those without the genetic risk factors.	Both genetic and environmental factors display low or modest associations with multiple sclerosis. Hypothetically, gene–envir-onment interactions may exert much stronger effects. In this study, we investigated potential interactions between genetic risk factors and smoking in relation to risk of developing multiple sclerosis.	21303861	Details
TOR1A	SNP	rs2187668	PCR	MS	Disease risk	Tag SNPs were selected that captured the following HLA types: DQ2.2 (2 SNPs for DQ2.2 and one SNP to exclude DQ4 from the DQ2.2 group), DQ2.5 (1 SNP), DQ7 (1 SNP), and DQ8 (1 SNP) (see Table 3). DQ2.5 and DQ8 are risk factors for CD and are carried by ,95% of CD patients [4,22]. The HLA-DQA1*0505 allele of DQ7 and HLA-DQA1*0501 allele of DQ2.5 only differ by one or a few base pairs and are thought to have the same functional properties. This also holds for the HLA-DQB1*0202 allele of DQ2.2 and the HLA-DQB1*0201 allele of DQ2.5. Most of the CD patients who do not carry DQ2.5 or DQ8, carry half of the DQ2.5 or DQ2.2 molecule (that is either HLA-DQA1*05 or DQB1*0202) suggesting that carrying part of the risk molecules has functional implications for the risk of CD	The HLA genes, located in the MHC region on chromosome 6p21.3, play an important role in many autoimmune disorders, such as celiac disease (CD), type 1 diabetes (T1D), rheumatoid arthritis, multiple sclerosis, psoriasis and others. Known HLA variants that confer risk to CD, for example, include DQA1*05/DQB1*02 (DQ2.5) and DQA1*03/ DQB1*0302 (DQ8). To diagnose the majority of CD patients and to study disease susceptibility and progression, typing these strongly associated HLA risk factors is of utmost importance.	18509540	Details
TRA	polymorphism	TCRAC1	PCR	MS	disease risk	Although the HLA DR2 genotype was significantly associated with MS, no interactive effects were seen with MS, DR2, TCRAC1, TCRBC2 and TCRBV alleles.	N/A	7911477	Details
GC	phenotype	Gc2/Gc2	PCR	MS	Disease risk	Moreover, the three major electrophoretic variants of the VDBP, Gc1f, Gc1s, and Gc2, did not differ between MS patients and control group	VDBP has a role in immune system as a chemotactic factor for neutrophil leucocytes and osteoclast activation.	27904983	Details
Cia5	Chromosome	N/A	PCR	EAE	Disease risk	Linkage between previously described arthritis QTL and MOG-induced EAE disease phenotypes	Quantitative trait loci (QTL) controlling inflammatory diseases	9692888	Details
HLA-DQA1	polymorphism	DQA1*0103	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
NR3C1	polymorphisms	rs6196(TT)	PCR	MS	Phenotypic risk	None of the identified alleles/genotypes were found to be associated with the severity of disease, response to glucocorticoids and disease subtypes.	N/A	27000245	Details
MOG	aminoacid substitution	a G→A transition occurring in exon 3 of the human MOG gene.	PCR	MS	Disease risk	It is therefore unlikely that the MOG Val 145 lle variant is responsible for genetic susceptibility to MS.	N/A	9493637	Details
TRBV20OR9-2	restriction fragments length polymorphisms (RFLP)	NA	PCR	MS	Disease risk	Our data suggest that the TcR/3 chain gene complex contains one or more genes involved in genetic susceptibility to develop MS	We found the distribution of the TcR haplotypes defined by the alleles of the three loci studied in the MS patients was significantly different from that found in control individuals. The distribution of TcR haplotypes in R / R MS patients was also different from that observed in controls.	8104194	Details
HLA-DRB1	Allele	NA	PCR	MS	Disease risk	These findings strongly imply that differences among HLA-DRB1*15 haplotypes will furnish the basis differences among HLA-DRB1*15 haplotypes will furnish the basis that the MHC haplotype is the fundamental unit of genetic control of immune response.	HLA-DRB1 alleles, constituting the strongest MS suscepti-bility factors, have been widely exploited in research including construction of transgenic animal models of MS.	18765817	Details
TOR1A	SNP	rs4639334	PCR	MS	Disease risk	Tag SNPs were selected that captured the following HLA types: DQ2.2 (2 SNPs for DQ2.2 and one SNP to exclude DQ4 from the DQ2.2 group), DQ2.5 (1 SNP), DQ7 (1 SNP), and DQ8 (1 SNP) (see Table 3). DQ2.5 and DQ8 are risk factors for CD and are carried by ,95% of CD patients [4,22]. The HLA-DQA1*0505 allele of DQ7 and HLA-DQA1*0501 allele of DQ2.5 only differ by one or a few base pairs and are thought to have the same functional properties. This also holds for the HLA-DQB1*0202 allele of DQ2.2 and the HLA-DQB1*0201 allele of DQ2.5. Most of the CD patients who do not carry DQ2.5 or DQ8, carry half of the DQ2.5 or DQ2.2 molecule (that is either HLA-DQA1*05 or DQB1*0202) suggesting that carrying part of the risk molecules has functional implications for the risk of CD	The HLA genes, located in the MHC region on chromosome 6p21.3, play an important role in many autoimmune disorders, such as celiac disease (CD), type 1 diabetes (T1D), rheumatoid arthritis, multiple sclerosis, psoriasis and others. Known HLA variants that confer risk to CD, for example, include DQA1*05/DQB1*02 (DQ2.5) and DQA1*03/ DQB1*0302 (DQ8). To diagnose the majority of CD patients and to study disease susceptibility and progression, typing these strongly associated HLA risk factors is of utmost importance.	18509540	Details
TNF	polymorphism	TNF2	PCR	MS	phenotypics risk	No significant differences were observed when the 3 MS subtypes were compared to each other.	Which also suggested that heterozygosity for the rare TNF2 allele, that is, the A/G genotype, confers protection against MS.	17268200	Details
GC	phenotype	Gc1F/Gc1F	PCR	MS	Disease risk	Moreover, the three major electrophoretic variants of the VDBP, Gc1f, Gc1s, and Gc2, did not differ between MS patients and control group	VDBP has a role in immune system as a chemotactic factor for neutrophil leucocytes and osteoclast activation.	27904983	Details
HLA-DQA1	polymorphism	DQA1*0301/2	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
NR3C1	polymorphisms	rs6196(TC)	PCR	MS	Phenotypic risk	None of the identified alleles/genotypes were found to be associated with the severity of disease, response to glucocorticoids and disease subtypes.	N/A	27000245	Details
ESR1	Alleles	NA	PCR	MS	Disease risk	Our results do not support a role for these two ESR1 markers in multiple sclerosis susceptibility, however other markers within ESR1 should not be excluded for potential involvement in the disorder.	Negative	17109894	Details
FCRL3	SNP	rs7528684	PCR	MS	Disease risk	Genotype and allele frequencies of two SNPs (rs7528684/FCRL3_3 and rs7522061/N28D), which were in high linkage disequilibrium (r2 = 0.87), differed between MS cases and controls. The	Some polymorphisms in the FCRL3 gene, a member of the Fc-receptor like family, have been associated with several autoimmune diseases and recently with multiple sclerosis (MS). We performed a case–control study of three SNPs in FCRL3 gene in 645 MS patients and 786 controls,	18313765	Details
TOR1A	SNP	rs7454108	PCR	MS	Disease risk	Tag SNPs were selected that captured the following HLA types: DQ2.2 (2 SNPs for DQ2.2 and one SNP to exclude DQ4 from the DQ2.2 group), DQ2.5 (1 SNP), DQ7 (1 SNP), and DQ8 (1 SNP) (see Table 3). DQ2.5 and DQ8 are risk factors for CD and are carried by ,95% of CD patients [4,22]. The HLA-DQA1*0505 allele of DQ7 and HLA-DQA1*0501 allele of DQ2.5 only differ by one or a few base pairs and are thought to have the same functional properties. This also holds for the HLA-DQB1*0202 allele of DQ2.2 and the HLA-DQB1*0201 allele of DQ2.5. Most of the CD patients who do not carry DQ2.5 or DQ8, carry half of the DQ2.5 or DQ2.2 molecule (that is either HLA-DQA1*05 or DQB1*0202) suggesting that carrying part of the risk molecules has functional implications for the risk of CD	The HLA genes, located in the MHC region on chromosome 6p21.3, play an important role in many autoimmune disorders, such as celiac disease (CD), type 1 diabetes (T1D), rheumatoid arthritis, multiple sclerosis, psoriasis and others. Known HLA variants that confer risk to CD, for example, include DQA1*05/DQB1*02 (DQ2.5) and DQA1*03/ DQB1*0302 (DQ8). To diagnose the majority of CD patients and to study disease susceptibility and progression, typing these strongly associated HLA risk factors is of utmost importance.	18509540	Details
PTPRC	polymorphism	C77G	PCR	MS	disease risk	This study reveals no evidence to suggest that these markers are associated with MS in the tested Australian Caucasian population.	N/A	19111528	Details
BDNF	polymorphisms	196 G/G	PCR	MS	Disease risk	In females, the same 270C/T genotype conferred a highly significant risk of MS, whereas the 196G/G genotype was associated with a less pronounced but still significantly increased risk of MS.	contribute to neuronal survival, axonal and neuronal repair	18061279	Details
HLA-DQA1	polymorphism	*0102	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
NR3C1	polymorphisms	rs6196(CC)	PCR	MS	Phenotypic risk	None of the identified alleles/genotypes were found to be associated with the severity of disease, response to glucocorticoids and disease subtypes.	N/A	27000245	Details
KLRB1	SNP	rs4763655	PCR	MS	Disease risk	We could confirm a marginally significant association between rs4763655 and MS (P=0.046, odds ratio=1.06 (1.00–1.13)) in a large Scandinavian case–control study of 5367 MS patients and 4485 controls.	N/A	21610746	Details
APOE	Gene polymorphisms	112C/R	PCR	MS	Disease risk	Thus, our results show that APOE gene polymor-phism is associated with the risk of MS development inethnic Tatars	A combined effect of APOE and IL1B allelic variants has been discovered indicating the increased risk of the disease development in the carriers of APOE*4 and IL1B*T/*T alleles	18664147	Details
HLA-DQB1	Alleles	NA	PCR	MS	Disease risk	In addition, primarily chronic pro-gressive MS was positively associated with theDQBl restriction fragment pattern seen in DR4,DQw8, DR7,DQw9, and DRw8, DQw4 haplotypes, as well as negatively associated with the Taq I DQBI allelic pattern corresponding to the serological specificity DQw7.	In addition, primarily chronic pro-gressive MS was positively associated with theDQBl restriction fragment pattern seen in DR4,DQw8, DR7,DQw9, and DRw8, DQw4 haplotypes, as well as negatively associated with the Taq I DQBI allelic pattern corresponding to the serological specificity DQw7.	2571150	Details
FCRL3	SNP	rs7522061	PCR	MS	Disease risk	Genotype and allele frequencies of two SNPs (rs7528684/FCRL3_3 and rs7522061/N28D), which were in high linkage disequilibrium (r2 = 0.87), differed between MS cases and controls. The	Some polymorphisms in the FCRL3 gene, a member of the Fc-receptor like family, have been associated with several autoimmune diseases and recently with multiple sclerosis (MS). We performed a case–control study of three SNPs in FCRL3 gene in 645 MS patients and 786 controls,	18313765	Details
TOR1A	SNP	rs4713586	PCR	MS	Disease risk	At first the sensitivity and specificity for DQ2.2 was high and accurate but the predictive value was low. The SNPs for DQ2.2 (rs2395182, rs7775228) not only tagged DQ2.2 but also included the relatively infrequent DQ4 allele. We therefore decided to tag DQ4 as well (rs4713586) making it possible to call a person DQ2.2 when the alleles were positive for DQ2.2 and negative for DQ4	The HLA genes, located in the MHC region on chromosome 6p21.3, play an important role in many autoimmune disorders, such as celiac disease (CD), type 1 diabetes (T1D), rheumatoid arthritis, multiple sclerosis, psoriasis and others. Known HLA variants that confer risk to CD, for example, include DQA1*05/DQB1*02 (DQ2.5) and DQA1*03/ DQB1*0302 (DQ8). To diagnose the majority of CD patients and to study disease susceptibility and progression, typing these strongly associated HLA risk factors is of utmost importance.	18509540	Details
PTPRC	polymorphism	C772T	PCR	MS	disease risk	This study reveals no evidence to suggest that these markers are associated with MS in the tested Australian Caucasian population.	N/A	19111528	Details
BDNF	polymorphisms	196 G/A	PCR	MS	Disease risk	In males, the 270C/T genotype (C270T BDNF polymorphism) was associated with a significantly increased risk of MS, whereas the G196A BDNF polymorphism did not confer an increased risk of MS.	contribute to neuronal survival, axonal and neuronal repair	18061279	Details
HLA-DQA1	polymorphism	*0201	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
NR3C1	allel	rs6196(T)	PCR	MS	Phenotypic risk	None of the identified alleles/genotypes were found to be associated with the severity of disease, response to glucocorticoids and disease subtypes.	N/A	27000245	Details
GSTT1	genotype	M1/T1	PCR	MS	Disease risk	The findings demonstrated a highly significant association between the null genotypes and MS (OR = 6.89 for M1/T1).	According to this study, it can be proposed that people with GSTM1 and GSTT1 deletions are at a higher risk for developing MS, which can be due to a decrease in enzymatic activity and their levels in nerve cells and the brain.	29055472	Details
APOE	Gene polymorphisms	158R/C	PCR	MS	Disease risk	Thus, our results show that APOE gene polymor-phism is associated with the risk of MS development inethnic Tatars	A combined effect of APOE and IL1B allelic variants has been discovered indicating the increased risk of the disease development in the carriers of APOE*4 and IL1B*T/*T alleles	18664147	Details
HLA-DRB1	Alleles	NA	PCR	MS	Disease risk	Both clinical forms of MS were found to be associated with the DRw15,DQw6 haplotpe.	Both clinical forms of MS were found to be associated with the DRw15,DQw6 haplotpe.	2571150	Details
FCRL3	SNP	rs11264799	PCR	MS	Disease risk	The C allele of FCRL3_3 was found to be protective for MS (per allele OR = 0.81, 95% C.I. = 0.70–0.94; P-value = 0.007) as was the G variant of N28D, but no association was found for rs11264799/FCRL3_4.	Some polymorphisms in the FCRL3 gene, a member of the Fc-receptor like family, have been associated with several autoimmune diseases and recently with multiple sclerosis (MS). We performed a case–control study of three SNPs in FCRL3 gene in 645 MS patients and 786 controls,	18313765	Details
CIITA	SNP	rs3087456	PCR	MS	Disease risk	No significant association of the SNP with MG was detected, neither in the patient group as a whole, nor in any clinical subgroup. The vast majority of previous replication studies have also not found an association of the SNP with autoimmune disorders	The major histocompatibility complex class II transactivator (CIITA) regulates MHC class II gene expression	20942939	Details
HLA-C	polymorphism	260-bp allele (allele 13)	PCR	MS	treatment risk	Most(90%) of the juvenile MS patients belonged to the relapsing-remitting subgroup, which itself showed a frequency of 28.5% of the 260-bp allele (n = 121, p = 0.045).	N/A	10344796	Details
BDNF	polymorphisms	270 C/C	PCR	MS	Disease risk	Our results show that C270T and G196A BDNF polymorphisms may affect susceptibility to and onset of MS.	contribute to neuronal survival, axonal and neuronal repair	18061279	Details
HLA-DQA1	polymorphism	*0401	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
NR3C1	allel	rs6196(C)	PCR	MS	Phenotypic risk	None of the identified alleles/genotypes were found to be associated with the severity of disease, response to glucocorticoids and disease subtypes.	N/A	27000245	Details
GSTM1	genotype	M1/T1	PCR	MS	Disease risk	The findings demonstrated a highly significant association between the null genotypes and MS (OR = 6.89 for M1/T1).	According to this study, it can be proposed that people with GSTM1 and GSTT1 deletions are at a higher risk for developing MS, which can be due to a decrease in enzymatic activity and their levels in nerve cells and the brain.	29055472	Details
IL1B	Gene polymorphisms	–511T/C	PCR	MS	Disease risk	Further-more, our data suggest the importance of –511T/C poly-morphism of IL1B gene in the predisposition for theMS development	A combined effect of APOE and IL1B allelic variants has been discovered indicating the increased risk of the disease development in the carriers of APOE*4 and IL1B*T/*T alleles	18664147	Details
HLA-DQA1	Alleles	NA	PCR	MS	Disease risk	In addition, primarily chronic pro-gressive MS was positively associated with theDQBl restriction fragment pattern seen in DR4,DQw8, DR7,DQw9, and DRw8, DQw4 haplotypes, as well as negatively associated with the Taq I DQBI allelic pattern corresponding to the serological specificity DQw7.	In addition, primarily chronic pro-gressive MS was positively associated with theDQBl restriction fragment pattern seen in DR4,DQw8, DR7,DQw9, and DRw8, DQw4 haplotypes, as well as negatively associated with the Taq I DQBI allelic pattern corresponding to the serological specificity DQw7.	2571150	Details
IL7R	SNP	rs6897932	PCR	MS	Disease risk	The T-allele in the single nucleotide polymorphism rs6897932 in the gene encoding the IL-7 receptor a (IL7RA) is associated with reduced risk of autoimmune diseases including multiple sclerosis and also affects the course of HIV infection. Low-grade inflammation (LGI) and self-reported, health-related quality of life (HRQL) are often associated with chronic diseases and widely used in assessing and monitoring health status. The aim of the present study was to evaluate whether the T-allele in rs6897932 is associated with reduced risk of LGI (hsCRP 3–10 mg/L), history of infectious mononucleosis (IM), and HRQL in healthy individuals. A total of 17, 293 healthy Danish individuals from the Danish Blood Donor Study were included in the analyses. We tested rs6897932 as a predictor of LGI, self-reported IM, and HRQL in univariable and multivariable models stratified by sex. No associations between rs6897932 and LGI, self-reported IM or HRQL were found in men or women.	Th e gene encoding IL-7Ra (IL7RA) is polymorphic, and single nucleotide polymorphisms (SNPs) in IL7RA have recently been associated with a wide range of diseases	25421942	Details
MT-ND1	SNP	NDUFS5	PCR	MS	phenotypics risk	SNP haplotypes within Complex I genes are associated with MS.	Complex I variants more likely influence a bioenergetic rather than an immune pathway.	15607211	Details
BDNF	polymorphisms	270 C/T	PCR	MS	Disease risk	Our results show that C270T and G196A BDNF polymorphisms may affect susceptibility to and onset of MS.	contribute to neuronal survival, axonal and neuronal repair	18061279	Details
HLA-DQA1	polymorphism	*0501	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
NR3C1	polymorphisms	rs6188(GG)	PCR	MS	Phenotypic risk	None of the identified alleles/genotypes were found to be associated with the severity of disease, response to glucocorticoids and disease subtypes.	N/A	27000245	Details
GSTT1	genotype	M1/T1	PCR	MS	Phenotypic risk	The null genotypes were found to be more frequent in women than in men. Moreover, a significant association was observed between the null genotype and EDSS 6–10 (OR = 3.199).	According to this study, it can be proposed that people with GSTM1 and GSTT1 deletions are at a higher risk for developing MS, which can be due to a decrease in enzymatic activity and their levels in nerve cells and the brain.	29055472	Details
HLA-DQB2	Alleles	NA	PCR	MS	Disease risk	In addition, primarily chronic pro-gressive MS was positively associated with theDQBl restriction fragment pattern seen in DR4,DQw8, DR7,DQw9, and DRw8, DQw4 haplotypes, as well as negatively associated with the Taq I DQBI allelic pattern corresponding to the serological specificity DQw7.	In addition, primarily chronic pro-gressive MS was positively associated with theDQBl restriction fragment pattern seen in DR4,DQw8, DR7,DQw9, and DRw8, DQw4 haplotypes, as well as negatively associated with the Taq I DQBI allelic pattern corresponding to the serological specificity DQw7.	2571150	Details
MBP	Allele	NA	PCR	MS	Disease risk	The myelin basic protein (MBP) gene is a candidate locus for susceptibility to multiple sclerosis.	The present data thus provide no evidence for a contribution ofthe MBP gene to multiple sclerosis susceptibility in French patients.	11197688	Details
AQP4	SNP	rs1839318	PCR	MS、BON、LETM、RON	Disease risk	A plasmid with the identified new missense mutation was constructed, and human embryonic kidney cells (HEK293A) were transfected with either the pEGFP-N1-AQP4-M23 vector (bearing the identified mutated cDNA sequence) or with the plasmid bearing the wild-type AQP4 gene sequence. AQP4 protein expression was analyzed in both experimental groups using Western Blot analysis following protein extraction from transfected cells. A synonymous mutation (rs1839318) was detected on exon 3, and an additional synonymous mutation was detected on the exon 2-2 (rs72557968). Most importantly, a new missense mutation was detected on exon 2-1. According to Western blot analysis, the mutated cDNA sequence yielded increased AQP4 protein expression in comparison with the wild-type cDNA sequence (P<0.05). AQP4 gene mutations are uncommon, occurring in only 3 out of 67 patients.	The purpose of this study was to determine whether or not aquaporin-4 (AQP4) gene mutations are related to the pathogenesis of inflammatory demyelinating diseases in the central nervous system. Polymorphisms of AQP4 exons 1–5 were determined by sequencing DNA from 67 patients with central nervous system inflammatory demyelinating diseases, including neuromyelitis optica (NMO), multiple sclerosis, recurrent or simultaneous bilateral optic neuritis, and longitudinally extensive transverse myelitis	25895050	Details
MT-ND1	SNP	NDUFS7	PCR	MS	phenotypics risk	SNP haplotypes within Complex I genes are associated with MS.	Complex I variants more likely influence a bioenergetic rather than an immune pathway.	15607211	Details
HLA-DQA1	polymorphism	*0601	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
NR3C1	polymorphisms	rs6188(GT)	PCR	MS	Phenotypic risk	None of the identified alleles/genotypes were found to be associated with the severity of disease, response to glucocorticoids and disease subtypes.	N/A	27000245	Details
GSTM1	genotype	M1/T1	PCR	MS	Phenotypic risk	The null genotypes were found to be more frequent in women than in men. Moreover, a significant association was observed between the null genotype and EDSS 6–10 (OR = 3.199).	According to this study, it can be proposed that people with GSTM1 and GSTT1 deletions are at a higher risk for developing MS, which can be due to a decrease in enzymatic activity and their levels in nerve cells and the brain.	29055472	Details
AQP4	SNP	rs72557968	PCR	MS、BON、LETM、RON	Disease risk	A plasmid with the identified new missense mutation was constructed, and human embryonic kidney cells (HEK293A) were transfected with either the pEGFP-N1-AQP4-M23 vector (bearing the identified mutated cDNA sequence) or with the plasmid bearing the wild-type AQP4 gene sequence. AQP4 protein expression was analyzed in both experimental groups using Western Blot analysis following protein extraction from transfected cells. A synonymous mutation (rs1839318) was detected on exon 3, and an additional synonymous mutation was detected on the exon 2-2 (rs72557968). Most importantly, a new missense mutation was detected on exon 2-1. According to Western blot analysis, the mutated cDNA sequence yielded increased AQP4 protein expression in comparison with the wild-type cDNA sequence (P<0.05). AQP4 gene mutations are uncommon, occurring in only 3 out of 67 patients.	The purpose of this study was to determine whether or not aquaporin-4 (AQP4) gene mutations are related to the pathogenesis of inflammatory demyelinating diseases in the central nervous system. Polymorphisms of AQP4 exons 1–5 were determined by sequencing DNA from 67 patients with central nervous system inflammatory demyelinating diseases, including neuromyelitis optica (NMO), multiple sclerosis, recurrent or simultaneous bilateral optic neuritis, and longitudinally extensive transverse myelitis	25895050	Details
MT-ND1	SNP	NDUFA7	PCR	MS	phenotypics risk	SNP haplotypes within Complex I genes are associated with MS.	Complex I variants more likely influence a bioenergetic rather than an immune pathway.	15607211	Details
HLA-DQB1	polymorphism	DQB1*0501	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
NR3C1	polymorphisms	rs6188(TT)	PCR	MS	Phenotypic risk	None of the identified alleles/genotypes were found to be associated with the severity of disease, response to glucocorticoids and disease subtypes.	N/A	27000245	Details
GSTT1	genotype	M1/T1	PCR	MS	Phenotypic risk	No significant association was noticed between MS type and the studied genotypes.	According to this study, it can be proposed that people with GSTM1 and GSTT1 deletions are at a higher risk for developing MS, which can be due to a decrease in enzymatic activity and their levels in nerve cells and the brain.	29055472	Details
IL1RN	Alleles	NA	PCR	MS	Disease risk	Our results are the first to implicate the IL-lra gene in susceptibility to multiple sclerosis.	DNA within the second intron of the IL-lra gene, which contains variable numbers of an identical repeat of 86 base-pairs, was amplified by PCR (details available from authors).	7564774	Details
STAT4	SNP	rs7574865	PCR	NMOSD	Disease risk	Given that NMOSD have complex genetic backgrounds, no single gene could independently trigger the autoimmune response and be alone responsible for NMOSD pathogenesis. In addition to STAT4, multiple non-HLA genes, such as PD-1, CYP7A1, CD58, FCRL3, and CD40, have been shown to be associated with increased NMOSD risk; most of these genes have been implicated in other autoimmune diseases	Chi-square tests and logistic regression analyses were performed with four genetic models, including allelic, additive, dominant, and recessive models, to identify associations with NMOSD	28852993	Details
TRA	polymorphism	Val	PCR	MS	disease risk	Among 30 informa tive families, there was no significant increase in haplotypes shared by affected siblings over that expected based on random segregation.	N/A	1387654	Details
HLA-DQB1	polymorphism	DQB1*0602	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
NR3C1	allel	rs6188(G)	PCR	MS	Phenotypic risk	None of the identified alleles/genotypes were found to be associated with the severity of disease, response to glucocorticoids and disease subtypes.	N/A	27000245	Details
GSTM1	genotype	M1/T1	PCR	MS	Phenotypic risk	No significant association was noticed between MS type and the studied genotypes.	According to this study, it can be proposed that people with GSTM1 and GSTT1 deletions are at a higher risk for developing MS, which can be due to a decrease in enzymatic activity and their levels in nerve cells and the brain.	29055472	Details
EIF2B1	Allele	NA	PCR	MS	Disease risk	We found no difference in the frequencies of 15 EIF2B1-5 variants between patients with MS and healthy controls, and none of the variants showed significant deviation of the Hardy-Weinberg equilibrium.Furthermore, sequencing data of EIF2B1-5 in 20 patients with MS and measurement of the activity of eIF2B complex in patient-derived lymphoblasts did not support our hypothesis	We found no difference in the frequencies of 15 EIF2B1-5 variants between patients with MS and healthy controls, and none of the variants showed significant deviation of the Hardy-Weinberg equilibrium.Furthermore, sequencing data of EIF2B1-5 in 20 patients with MS and measurement of the activity of eIF2B complex in patient-derived lymphoblasts did not support our hypothesis	18632786	Details
STAT4	SNP	rs10181656	PCR	NMOSD	Disease risk	Given that NMOSD have complex genetic backgrounds, no single gene could independently trigger the autoimmune response and be alone responsible for NMOSD pathogenesis. In addition to STAT4, multiple non-HLA genes, such as PD-1, CYP7A1, CD58, FCRL3, and CD40, have been shown to be associated with increased NMOSD risk; most of these genes have been implicated in other autoimmune diseases	Chi-square tests and logistic regression analyses were performed with four genetic models, including allelic, additive, dominant, and recessive models, to identify associations with NMOSD	28852993	Details
TRA	polymorphism	Va6	PCR	MS	disease risk	Among 30 informa tive families, there was no significant increase in haplotypes shared by affected siblings over that expected based on random segregation.	N/A	1387654	Details
HLA-DQB1	polymorphism	DQB1*0302	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
NR3C1	allel	rs6188(T)	PCR	MS	Phenotypic risk	None of the identified alleles/genotypes were found to be associated with the severity of disease, response to glucocorticoids and disease subtypes.	N/A	27000245	Details
ARHGAP45	polymorphisms	HA-1 1500/504(CA,CA/TG,TG)	PCR	MS	Disease risk	In cohorts of patients with systemic lupus erythematosus, rheumatoid arthritis and multiple sclerosis, no significant differences in the frequencies of ABCA7 and HA-1 allelic variants were observed relative to controls.	N/A	15593299	Details
EIF2B5	SNP	rs2971410	PCR	MS	Disease risk	We found no difference in the frequencies of 15 EIF2B1-5 variants between patients with MS and healthy controls, and none of the variants showed significant deviation of the Hardy-Weinberg equilibrium.Furthermore, sequencing data of EIF2B1-5 in 20 patients with MS and measurement of the activity of eIF2B complex in patient-derived lymphoblasts did not support our hypothesis	We found no difference in the frequencies of 15 EIF2B1-5 variants between patients with MS and healthy controls, and none of the variants showed significant deviation of the Hardy-Weinberg equilibrium.Furthermore, sequencing data of EIF2B1-5 in 20 patients with MS and measurement of the activity of eIF2B complex in patient-derived lymphoblasts did not support our hypothesis	18632786	Details
STAT4	SNP	rs7601754	PCR	NMOSD	Disease risk	Given that NMOSD have complex genetic backgrounds, no single gene could independently trigger the autoimmune response and be alone responsible for NMOSD pathogenesis. In addition to STAT4, multiple non-HLA genes, such as PD-1, CYP7A1, CD58, FCRL3, and CD40, have been shown to be associated with increased NMOSD risk; most of these genes have been implicated in other autoimmune diseases	Chi-square tests and logistic regression analyses were performed with four genetic models, including allelic, additive, dominant, and recessive models, to identify associations with NMOSD	28852993	Details
HLA-DQB1	polymorphism	*0502-*0504	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
ATG5	polymorphisms	rs2245214(GG/GC/CC)	PCR	MS	Disease risk	However, no association was found between ATG5 variants and MS patients.	N/A	24953774	Details
ARHGAP45	polymorphisms	HA-1 865(T,T/A,A)	PCR	MS	Disease risk	In cohorts of patients with systemic lupus erythematosus, rheumatoid arthritis and multiple sclerosis, no significant differences in the frequencies of ABCA7 and HA-1 allelic variants were observed relative to controls.	N/A	15593299	Details
EIF2B5	SNP	rs2893756	PCR	MS	Disease risk	We found no difference in the frequencies of 15 EIF2B1-5 variants between patients with MS and healthy controls, and none of the variants showed significant deviation of the Hardy-Weinberg equilibrium.Furthermore, sequencing data of EIF2B1-5 in 20 patients with MS and measurement of the activity of eIF2B complex in patient-derived lymphoblasts did not support our hypothesis	We found no difference in the frequencies of 15 EIF2B1-5 variants between patients with MS and healthy controls, and none of the variants showed significant deviation of the Hardy-Weinberg equilibrium.Furthermore, sequencing data of EIF2B1-5 in 20 patients with MS and measurement of the activity of eIF2B complex in patient-derived lymphoblasts did not support our hypothesis	18632786	Details
STAT4	SNP	rs10168266	PCR	NMOSD	Disease risk	Given that NMOSD have complex genetic backgrounds, no single gene could independently trigger the autoimmune response and be alone responsible for NMOSD pathogenesis. In addition to STAT4, multiple non-HLA genes, such as PD-1, CYP7A1, CD58, FCRL3, and CD40, have been shown to be associated with increased NMOSD risk; most of these genes have been implicated in other autoimmune diseases	Chi-square tests and logistic regression analyses were performed with four genetic models, including allelic, additive, dominant, and recessive models, to identify associations with NMOSD	28852993	Details
HLA-DQB1	polymorphism	*0601	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
ATG5	allel	rs2245214(C/G)	PCR	MS	Disease risk	However, no association was found between ATG5 variants and MS patients.	N/A	24953774	Details
ARHGAP45	polymorphisms	HA-1 1403(G,G/A,A)	PCR	MS	Disease risk	In cohorts of patients with systemic lupus erythematosus, rheumatoid arthritis and multiple sclerosis, no significant differences in the frequencies of ABCA7 and HA-1 allelic variants were observed relative to controls.	N/A	15593299	Details
PTPRC	Allele	NA	PCR	MS	Disease risk	No PTPRC exon 4 genomic mutations were seen in any of the five families. In the non-familial cases the incidence of mutation was 4.1% in 197 controls and 5.1% in 330 multiple sclerosis patients.No significant association was found in this study with this mutation and disease susceptibility, sex, or an extended disability scale score of < 5.5.	This candidate does not appear to influence the development of familial multiple sclerosis in this population. The negative result could arise from a type II error owing to the number of families and non-familial cases screened. Alternatively it might suggest that the contribution of the PTPRC mutation depends upon the genetic background.	12810785	Details
STAT4	SNP	rs13426947	PCR	NMOSD	Disease risk	Given that NMOSD have complex genetic backgrounds, no single gene could independently trigger the autoimmune response and be alone responsible for NMOSD pathogenesis. In addition to STAT4, multiple non-HLA genes, such as PD-1, CYP7A1, CD58, FCRL3, and CD40, have been shown to be associated with increased NMOSD risk; most of these genes have been implicated in other autoimmune diseases	Chi-square tests and logistic regression analyses were performed with four genetic models, including allelic, additive, dominant, and recessive models, to identify associations with NMOSD	28852993	Details
NOS1	allel	N/A	PCR	MS	Disease risk	no significant differences in allele frequencies were detected between MS patients and controls.	N/A	16143043	Details
HLA-DQB1	polymorphism	*0603-*0605	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
ATG5	polymorphisms	rs548234(TT/CC/TC)	PCR	MS	Disease risk	However, no association was found between ATG5 variants and MS patients.	N/A	24953774	Details
ABCA7	polymorphisms	ABCA7 955(A, A/G, G)	PCR	MS	Disease risk	In cohorts of patients with systemic lupus erythematosus, rheumatoid arthritis and multiple sclerosis, no significant differences in the frequencies of ABCA7 and HA-1 allelic variants were observed relative to controls.	N/A	15593299	Details
SYN3	SNP	rs133946	PCR	MS	Disease risk	In summary, our data do not support the reported association for Italian MS patients or a protective effect of the C/A haplotype for the German cohort investigated here.	Plausible explanations for the differences described might include varying allelic distributions of the investigated polymorphisms due to different geographical origins of the cohorts, i.e., Italian MS vs. German MS patients and controls, respectively	N/A	Details
IL7R	SNP	rs11567686	PCR	MS	Phenotypic risk	In conclusion, this is the first study to show a significant association between the IL7R promoter polymorphisms and the age of onset of MS	On the cell surface,cytokine form a complex where they induce the maturation of IL7R and IL7 B and T cells, and play a crucial role on the peripherical T cell hemostasis and immune tolerance	30443838	Details
MGMT	gene polymorphisms	N/A	PCR	PML 、MS 、toxoplasmosis、cytomegalovirus infection、HSV1 encephalitis、 HIV infection、with mycosis and encephalitis、brain abscess、 central pontine/extrapontine myelinolysis、 Wallerian degeneration 、glioma	Disease risk	his study demonstrates for the first time that one can indeed detect slightly enhanced MGMT promoter methylation in individual cases of inflammatory demyelinating CNS diseases such as multiple sclerosis and progressive multifocal leucencephalopathy (PML), as well as in other demyelinating diseases such as central pontine and exptrapontine myelinolysis, and diseases with myelin damage such as Wallerian degeneration. In this context, we identified a reduction in the expression of the demethylase TET1 as a possible cause for the enhanced MGMT promoter methylation	O6 -methylguanine-DNA methyltransferase (MGMT) is an important constitutively active enzyme which is expressed in every human cell, playing a pivotal role in the cellular defense against the toxicity of alkylating substances by removing methyl groups, particularly O6 -methylguanine residues, thereby repairing alkylated DNA and preventing mismatch errors during DNA replication	33917711	Details
NFKB2	allel	N/A	PCR	MS	Disease risk	no significant differences in allele frequencies were detected between MS patients and controls.	N/A	16143043	Details
HLA-DQB1	polymorphism	*02	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
ATG5	allel	rs548234(T/C)	PCR	MS	Disease risk	However, no association was found between ATG5 variants and MS patients.	N/A	24953774	Details
ABCA7	polymorphisms	ABCA7 4580(C, C/G, G)	PCR	MS	Disease risk	In cohorts of patients with systemic lupus erythematosus, rheumatoid arthritis and multiple sclerosis, no significant differences in the frequencies of ABCA7 and HA-1 allelic variants were observed relative to controls.	N/A	15593299	Details
SYN3	SNP	rs133945	PCR	MS	Disease risk	In summary, our data do not support the reported association for Italian MS patients or a protective effect of the C/A haplotype for the German cohort investigated here.	Plausible explanations for the differences described might include varying allelic distributions of the investigated polymorphisms due to different geographical origins of the cohorts, i.e., Italian MS vs. German MS patients and controls, respectively	N/A	Details
IL7R	SNP	rs11567685	PCR	MS	Phenotypic risk	In conclusion, this is the first study to show a significant association between the IL7R promoter polymorphisms and the age of onset of MS	On the cell surface,cytokine form a complex where they induce the maturation of IL7R and IL7 B and T cells, and play a crucial role on the peripherical T cell hemostasis and immune tolerance	30443838	Details
Ptpn22	DNA methylation	DNA methylation	PCR	MS	Disease risk	Based on our findings we conclude that antibody mediated T cell lymphopenia does not trigger overt auto-aggression in PTPN22 KO mice although PTPN22 deficient T cells showed a pronounced effector phenotype. High abundance of Tregs and IL-10 producing cells in PTPN22 KO mice have been previously associated with increased tolerance in a model of pancreatic islet transplantation and might suppress excessive T cell proliferation and keep activated T cell clones in check	We induced lymphopenia by treating wild-type or PTPN22 knock-out mice with T cell depleting antibodies and monitored reconstitution of the T cell pool. We found that PTPN22 deficient T cells acquired a more activated effector phenotype, with significantly more IFNγ producing cells. This resulted from expansion driven by self-peptide MHC, as it was evident when the contribution of IL-7 to lymphopenic expansion was blocked with IL-7R Ab	32047502	Details
FADD	allel	N/A	PCR	MS	Disease risk	no significant differences in allele frequencies were detected between MS patients and controls.	N/A	16143043	Details
HLA-DQB1	polymorphism	*0301	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
ATG5	polymorphisms	rs573775(TT/TC/CC)	PCR	MS	Disease risk	However, no association was found between ATG5 variants and MS patients.	N/A	24953774	Details
Mbp	Allele	NA	PCR	MS	Disease risk	We conclude that both MHC-controlled promoting and protective influences on EAE are dependent on certain MHC/MBP peptide combinations, and that the 87-110 region of MBP contains a major MHC-associated encephalitogenic epitope in the rat.	The myelin basic protein (MBP) peptide 63-88-induced experimental autoimmune encephalomyelitis (EAE) and its associated T cell cytokine profile are influenced by the rat major histocompatibility complex (MHC).	9209515	Details
IL7R	SNP	rs7718919	PCR	MS	Phenotypic risk	In conclusion, this is the first study to show a significant association between the IL7R promoter polymorphisms and the age of onset of MS	On the cell surface,cytokine form a complex where they induce the maturation of IL7R and IL7 B and T cells, and play a crucial role on the peripherical T cell hemostasis and immune tolerance	30443838	Details
USP18	SNP	rs2252257	PCR	NMOSD	Disease risk	The single-nucleotide polymorphism (SNP) rs2252257 in the promoter and enhancer of ubiquitin-specific peptidase USP18 was linked to familial NMOSD (p=7.8E-05, logarithm of the odds (LOD)=3.1), SNPs rs361553, rs2252257 and rs5746523 were related to sporadic NMOSD (p=1.29E-10, 3.45E-07 and 2.01E09, respectively). Patients with the SNP rs361553 T/T genotype had higher recurrence rate than C/T or C/C genotype (1.22±0.85 vs 0.69±0.57 and 0.81±0.65, p=0.003 and 0.001, respectively). SNPs rs361553 and rs2252257 altered USP18 expression in brain and nerve tissues.	USP18 gene consists of 11 exons and 10 introns	36376024	Details
GZMB	allel	N/A	PCR	MS	Disease risk	no significant differences in allele frequencies were detected between MS patients and controls.	N/A	16143043	Details
HLA-DQB1	polymorphism	*0303	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
ATG5	allel	rs573775(T/C)	PCR	MS	Disease risk	However, no association was found between ATG5 variants and MS patients.	N/A	24953774	Details
CYP2D6	Allele	NA	PCR	MS	Disease risk	These results indicate that mutations at the CYP2D6 gene do 1 not seem to be a factor in determining susceptibility to MS	Recent reports have shown association between CYP2D6 polymorphism and neuronal degenerative diseases such as Parkinson's disease.	8750111	Details
USP18	SNP	rs361553	PCR	NMOSD	Disease risk	The single-nucleotide polymorphism (SNP) rs2252257 in the promoter and enhancer of ubiquitin-specific peptidase USP18 was linked to familial NMOSD (p=7.8E-05, logarithm of the odds (LOD)=3.1), SNPs rs361553, rs2252257 and rs5746523 were related to sporadic NMOSD (p=1.29E-10, 3.45E-07 and 2.01E09, respectively). Patients with the SNP rs361553 T/T genotype had higher recurrence rate than C/T or C/C genotype (1.22±0.85 vs 0.69±0.57 and 0.81±0.65, p=0.003 and 0.001, respectively). SNPs rs361553 and rs2252257 altered USP18 expression in brain and nerve tissues.	USP18 gene consists of 11 exons and 10 introns	36376024	Details
ERBB3	allel	N/A	PCR	MS	Disease risk	no significant differences in allele frequencies were detected between MS patients and controls.	N/A	16143043	Details
HLA-DQB1	polymorphism	*0401-*0402	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
ATG5	polymorphisms	rs6568431(AA/AC/CC)	PCR	MS	Disease risk	However, no association was found between ATG5 variants and MS patients.	N/A	24953774	Details
Mbp	Allele	NA	PCR	MS	Disease risk	We conclude that the MBP gene does not influence susceptibility to MS in Swedish patients.	Myelin basic protein (MBP) is a potential autoantigen in multiple sclerosis (MS) and its gene therefore is an attractive candidate to confer genetic susceptibility to this disease. Linkage and association with certain alleles of a 1.2 kb tetranucleotide repeat region 5' to the MBP gene with MS have been reported in Finnish patients, and an association has been reported from Denmark.	9482678	Details
USP18	SNP	rs5746523	PCR	NMOSD	Disease risk	The single-nucleotide polymorphism (SNP) rs2252257 in the promoter and enhancer of ubiquitin-specific peptidase USP18 was linked to familial NMOSD (p=7.8E-05, logarithm of the odds (LOD)=3.1), SNPs rs361553, rs2252257 and rs5746523 were related to sporadic NMOSD (p=1.29E-10, 3.45E-07 and 2.01E09, respectively). Patients with the SNP rs361553 T/T genotype had higher recurrence rate than C/T or C/C genotype (1.22±0.85 vs 0.69±0.57 and 0.81±0.65, p=0.003 and 0.001, respectively). SNPs rs361553 and rs2252257 altered USP18 expression in brain and nerve tissues.	USP18 gene consists of 11 exons and 10 introns	36376024	Details
NGF	allel	N/A	PCR	MS	Disease risk	no significant differences in allele frequencies were detected between MS patients and controls.	N/A	16143043	Details
HLA-DRB1	polymorphism	DRB1*1502	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
ATG5	allel	rs6568431(A/C)	PCR	MS	Disease risk	However, no association was found between ATG5 variants and MS patients.	N/A	24953774	Details
MEFV	polymorphisms	E148Q	PCR	MS	Phenotypic risk	Our results indicate that MEFV gene mutations do not affect the neurologic prognosis in patients with MS.	N/A	24712487	Details
CCL2	Allele	NA	PCR	MS	Disease risk	Thus, our data could not reveal any association between the MCP-1 -2518 polymorphism and susceptibility to or clinical disease course of MS.	Cytokines and chemokines like the proinflammatory chemokine, monocytechemoattractant protein 1 (MCP-1) are important for the recruitment of inflammatory cells into multiple sclerosis (MS) lesion	15191525	Details
PARP1	allel	N/A	PCR	MS	Disease risk	no significant differences in allele frequencies were detected between MS patients and controls.	N/A	16143043	Details
HLA-DRB1	polymorphism	DRB1*04	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
ATG5	polymorphisms	rs6937876(GG/GA/AA)	PCR	MS	Disease risk	However, no association was found between ATG5 variants and MS patients.	N/A	24953774	Details
MEFV	polymorphisms	P369S	PCR	MS	Phenotypic risk	Our results indicate that MEFV gene mutations do not affect the neurologic prognosis in patients with MS.	N/A	24712487	Details
IL7R	SNP	rs6897932	PCR	MS	Disease risk	The allelic and genotypic estimated frequencies of a reported risk variant rs6897932 in patients and controls in our population confirmed its association with the disease (P= 0.009, OR = 6.273, for TT genotype). Also, we report a possible hazardous cutoff for changes in a potential exon splicing silencer element (ESS (nt. 20-24)) and its correlation with rs6897932 to confer the risk of developing MS.	Notably, it is important that other aspects of the exon splicing of the IL7RA gene be taken into consideration to understand the underling mechanism of the correlation between this changes and MS disease.	28582853	Details
AR	DNA methylation	DNA methylation	PCR	MS	Disease risk	The highly similar patterns of X chromosome inactivation among monochorionic twin pairs may result from their shared placental blood supply during intrauterine life. Alternatively, these patterns may indicate that X chromosome inactivation occurs before the twinning event in this anatomic subgroup of MZ twins. The data further suggest that these factors do not make a major contribution to the high discordance rates for autoimmune disease in MZ twin pairs	monochorionic twins share their fetal blood supply during gestation and thus share a common immune system. In particular, monochorionic twins would have in common the prenatal stochastic events associated with immunoglobulin and T cell receptor gene rearrangement , whereas dichorionic twin pairs would undergo these gene rearrangements independently of one another during fetal life	8790602	Details
GNB3	polymorphisms	C825T	PCR	MS	Disease risk	Apart from a trend to a reduced frequency of d32 CCR5 and increased GNB3 825T polymorphism in primary chronic progressive patients, numbers did not reach statistical significance in any group of MS.	influence autoreactive T-cell-actions like proliferation and chemotaxis across the blood–brain barrier via chemokine receptors (CCR) and G-protein coupled activating mechanisms.	12270649	Details
HLA-DRB1	polymorphism	*0101-*0102	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
ATG5	allel	rs6937876(G/A)	PCR	MS	Disease risk	However, no association was found between ATG5 variants and MS patients.	N/A	24953774	Details
MEFV	polymorphisms	F479L	PCR	MS	Phenotypic risk	Our results indicate that MEFV gene mutations do not affect the neurologic prognosis in patients with MS.	N/A	24712487	Details
S1PR1	DNA methylation	DNA methylation	PCR	autoimmune diseases	Disease risk	In summary, fi ndings in this study suggest that individual variations in S1P 1 may infl uence cardiovascular/immune functions as well as drug sensitivity and, therefore, infer differential risks for cardiovascular and autoimmune diseases as well as response to S1P receptor modulatory drugs. Suffi ciently powered prospective cohort studies should be conducted to validate possible relationships between individual variations in the S1P 1 receptor and specifi c diseases/drug sensitivity	One SNP mutant (Arg 120 to Pro) failed to transmit sphingosine 1-phosphate (S1P)-induced intracellular signals such as calcium increase and activation of p44/42 MAPK and Akt	25293589	Details
CCR5	mutation	d32	PCR	MS	Disease risk	Apart from a trend to a reduced frequency of d32 CCR5 and increased GNB3 825T polymorphism in primary chronic progressive patients, numbers did not reach statistical significance in any group of MS.	influence autoreactive T-cell-actions like proliferation and chemotaxis across the blood–brain barrier via chemokine receptors (CCR) and G-protein coupled activating mechanisms.	12270649	Details
HLA-DRB1	polymorphism	*1502	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
MEFV	polymorphisms	M680I (G/C)	PCR	MS	Phenotypic risk	Our results indicate that MEFV gene mutations do not affect the neurologic prognosis in patients with MS.	N/A	24712487	Details
IL10	Gene polymorphisms	L-10 - 1082	PCR	MS	Disease risk	The AG genotype of IL-10 proved to be protective against severe MS in all patients (OR=0.32, P=0.010), the effect being increased over the years	higher doses of IL-10 appear toinduce the expression of Th1 cytokines	14616291	Details
APOE	Allele	NA	PCR	MS	Disease risk	Our study demonstrates that two APOE polymor-phisms are not associated with occurrence of MS or accumulation of clinical burden over time in the largest cohort of MS patients studied to date	Apolipoprotein E (apoE) influences the high-affinity binding of low-density lipoproteins (LDL) to their receptor.	10489065	Details
FCRL3	SNP	rs7528684	PCR	Neuromyelitis optica (NMO)	Disease risk	Conclusions in the present study could be drawn that 4 SNPs in FCRL3 (FCRL3_3C, 5C, 6A, 8G) might account for increased risk of NMO in a Chinese-Han population. Nevertheless, further cohort studies are in demand to validate the association in the future	FCRL3 encoded a member of the immunoglobulin receptor superfamily, which could directly act against myelin-derived antigens.16 Furthermore, although the precise function of FCRL3 remains to be unknown, the contained immunoreceptor-tyrosine inhibitory motifs (ITIMs) and immunoreceptor-tyrosine activation motifs (ITAMs) are deemed to be involved in the regulation of the immune system	26402798	Details
IFNA17	polymorphism	N/A	PCR	MS	disease risk	Thus, our study does not support an association between the IFNA17 allele and risk for MS.	The finding, based on eight PPMS cases being positive for the allele whilst none of the referents were, may therefore be a post hoc type 1 error.	17956450	Details
ST8SIA1	SNP	rs704219	PCR	MS	Disease risk	Australia validated the association of ST8SIA1 in individuals with MS, showing transmission disequilibrium of the paternal alleles for three additional SNPs, namely rs704219, rs2041906, and rs1558793, with p = 0.001, p = 0.01 and p = 0.01 respectively.	ST8SIA1 encodes GD3 synthase, a ubiquitously expressed type II transmembrane protein that generates GD3 ganglioside (GD3G) by catalyzing the addition of a second sialic acid residue to its immediate precursor GM3.	18612409	Details
HLA-DRB1	polymorphism	*1601	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
MEFV	polymorphisms	I692 DEL	PCR	MS	Phenotypic risk	Our results indicate that MEFV gene mutations do not affect the neurologic prognosis in patients with MS.	N/A	24712487	Details
VDR	SNP	ApaI(rs7975232)	PCR	MS	Disease risk	AA genotype polymorphism ofApaIand BsmI (OR = 4.6 and OR= 2.52, respectively), CC genotype of TaqI (OR= 2.41) and AC genotype ofApaI (OR= 1.79) are associated with the disease status. Nevertheless, the results revealed the protective role of TT genotype of TaqI (ORs b 1), CC genotype of Apal, and GG genotype ofBsmI(ORs b 1)	negative	27423580	Details
TAP1	Gene polymorphisms	TAP1 - 1069	PCR	MS	Disease risk	No significant differences in the frequencies of TAP polymorphisms were observed between both groups	These data suggest that TAP is not a susceptibility gene for MS	7929801	Details
HLA-DRB1	Allele	NA	PCR	MS	Phenotypic risk	We suggest that DRB1*0103 is a necessary but not sufficient condition for the susceptibility for MS immunopathic trait in this family.	We studied two extended families in which not only multiple sclerosis (MS) segregates, but also approximately 18% of the cerebrospinal fluid (CSF) investigated blood relatives have ‘MS immunopathic trait’, an oligoclonal CSF immunopathy similar to that seen in MS, but with no neurological symptoms.	17262999	Details
FCRL3	SNP	rs11264799	PCR	Neuromyelitis optica (NMO)	Disease risk	Conclusions in the present study could be drawn that 4 SNPs in FCRL3 (FCRL3_3C, 5C, 6A, 8G) might account for increased risk of NMO in a Chinese-Han population. Nevertheless, further cohort studies are in demand to validate the association in the future	FCRL3 encoded a member of the immunoglobulin receptor superfamily, which could directly act against myelin-derived antigens.16 Furthermore, although the precise function of FCRL3 remains to be unknown, the contained immunoreceptor-tyrosine inhibitory motifs (ITIMs) and immunoreceptor-tyrosine activation motifs (ITAMs) are deemed to be involved in the regulation of the immune system	26402798	Details
TRA	polymorphism	N/A	PCR	MS	disease risk	We conclude there is no convincing evidence for an association of MS with TCR α, β, γ, and δ chain gene polymorphisms.	N/A	8857743	Details
ST8SIA1	SNP	rs2041906	PCR	MS	Disease risk	Australia validated the association of ST8SIA1 in individuals with MS, showing transmission disequilibrium of the paternal alleles for three additional SNPs, namely rs704219, rs2041906, and rs1558793, with p = 0.001, p = 0.01 and p = 0.01 respectively.	ST8SIA1 encodes GD3 synthase, a ubiquitously expressed type II transmembrane protein that generates GD3 ganglioside (GD3G) by catalyzing the addition of a second sialic acid residue to its immediate precursor GM3.	18612409	Details
HLA-DRB1	polymorphism	*0301	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
MEFV	polymorphisms	M694V	PCR	MS	Phenotypic risk	Our results indicate that MEFV gene mutations do not affect the neurologic prognosis in patients with MS.	N/A	24712487	Details
VDR	SNP	BsmI(rs1544410)	PCR	MS	Disease risk	AA genotype polymorphism ofApaIand BsmI (OR = 4.6 and OR= 2.52, respectively), CC genotype of TaqI (OR= 2.41) and AC genotype ofApaI (OR= 1.79) are associated with the disease status. Nevertheless, the results revealed the protective role of TT genotype of TaqI (ORs b 1), CC genotype of Apal, and GG genotype ofBsmI(ORs b 1)	positive	27423580	Details
TAP1	Gene polymorphisms	TAP1 - 1982	PCR	MS	Disease risk	No significant differences in the frequencies of TAP polymorphisms were observed between both groups	These data suggest that TAP is not a susceptibility gene for MS	7929801	Details
FCRL3	SNP	rs945635	PCR	Neuromyelitis optica (NMO)	Disease risk	Conclusions in the present study could be drawn that 4 SNPs in FCRL3 (FCRL3_3C, 5C, 6A, 8G) might account for increased risk of NMO in a Chinese-Han population. Nevertheless, further cohort studies are in demand to validate the association in the future	FCRL3 encoded a member of the immunoglobulin receptor superfamily, which could directly act against myelin-derived antigens.16 Furthermore, although the precise function of FCRL3 remains to be unknown, the contained immunoreceptor-tyrosine inhibitory motifs (ITIMs) and immunoreceptor-tyrosine activation motifs (ITAMs) are deemed to be involved in the regulation of the immune system	26402798	Details
TRB	polymorphism	N/A	PCR	MS	disease risk	We conclude there is no convincing evidence for an association of MS with TCR α, β, γ, and δ chain gene polymorphisms.	N/A	8857743	Details
ST8SIA1	SNP	rs1558793	PCR	MS	Disease risk	Australia validated the association of ST8SIA1 in individuals with MS, showing transmission disequilibrium of the paternal alleles for three additional SNPs, namely rs704219, rs2041906, and rs1558793, with p = 0.001, p = 0.01 and p = 0.01 respectively.	ST8SIA1 encodes GD3 synthase, a ubiquitously expressed type II transmembrane protein that generates GD3 ganglioside (GD3G) by catalyzing the addition of a second sialic acid residue to its immediate precursor GM3.	18612409	Details
HLA-DRB1	polymorphism	*0401-*0408	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
MEFV	polymorphisms	M694I	PCR	MS	Phenotypic risk	Our results indicate that MEFV gene mutations do not affect the neurologic prognosis in patients with MS.	N/A	24712487	Details
VDR	SNP	TaqI(rs731236)	PCR	MS	Disease risk	AA genotype polymorphism ofApaIand BsmI (OR = 4.6 and OR= 2.52, respectively), CC genotype of TaqI (OR= 2.41) and AC genotype ofApaI (OR= 1.79) are associated with the disease status. Nevertheless, the results revealed the protective role of TT genotype of TaqI (ORs b 1), CC genotype of Apal, and GG genotype ofBsmI(ORs b 1)	negative	27423580	Details
TAP2	Gene polymorphisms	TAP2 - 1231	PCR	MS	Disease risk	No significant differences in the frequencies of TAP polymorphisms were observed between both groups	These data suggest that TAP is not a susceptibility gene for MS	7929801	Details
FCRL3	SNP	rs3761959	PCR	Neuromyelitis optica (NMO)	Disease risk	Conclusions in the present study could be drawn that 4 SNPs in FCRL3 (FCRL3_3C, 5C, 6A, 8G) might account for increased risk of NMO in a Chinese-Han population. Nevertheless, further cohort studies are in demand to validate the association in the future	FCRL3 encoded a member of the immunoglobulin receptor superfamily, which could directly act against myelin-derived antigens.16 Furthermore, although the precise function of FCRL3 remains to be unknown, the contained immunoreceptor-tyrosine inhibitory motifs (ITIMs) and immunoreceptor-tyrosine activation motifs (ITAMs) are deemed to be involved in the regulation of the immune system	26402798	Details
TRG	polymorphism	N/A	PCR	MS	disease risk	We conclude there is no convincing evidence for an association of MS with TCR α, β, γ, and δ chain gene polymorphisms.	N/A	8857743	Details
HLA-DRB1	genotype	DR1	PCR	MS	Disease risk	There was no significant difference between any group of index cases and controls or affected females and male index cases or controls.	N/A	7853025	Details
HLA-DRB1	polymorphism	*11-*14	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
MEFV	polymorphisms	K695R	PCR	MS	Phenotypic risk	Our results indicate that MEFV gene mutations do not affect the neurologic prognosis in patients with MS.	N/A	24712487	Details
VDR	SNP	FokI(rs222870)	PCR	MS	Disease risk	AA genotype polymorphism ofApaIand BsmI (OR = 4.6 and OR= 2.52, respectively), CC genotype of TaqI (OR= 2.41) and AC genotype ofApaI (OR= 1.79) are associated with the disease status. Nevertheless, the results revealed the protective role of TT genotype of TaqI (ORs b 1), CC genotype of Apal, and GG genotype ofBsmI(ORs b 1)	positive	27423580	Details
TAP2	Gene polymorphisms	TAP2 - 2089	PCR	MS	Disease risk	No significant differences in the frequencies of TAP polymorphisms were observed between both groups	These data suggest that TAP is not a susceptibility gene for MS	7929801	Details
IL-2R	SNP	rs2104286	PCR	MS	Disease risk	Together, these data suggest that multiple mechanisms converge in disease leading to decreased response to IL-2, a phenotype that may eventually lead to loss of tolerance and autoimmunity	IL-2 receptor (IL-2R) signaling is essential for optimal stability and function of CD4+CD25hiFOXP3+ regulatory T cells (Treg); a cell type that plays an integral role in maintaining tolerance.	24376757	Details
FCRL3	SNP	rs2210913	PCR	Neuromyelitis optica (NMO)	Disease risk	Conclusions in the present study could be drawn that 4 SNPs in FCRL3 (FCRL3_3C, 5C, 6A, 8G) might account for increased risk of NMO in a Chinese-Han population. Nevertheless, further cohort studies are in demand to validate the association in the future	FCRL3 encoded a member of the immunoglobulin receptor superfamily, which could directly act against myelin-derived antigens.16 Furthermore, although the precise function of FCRL3 remains to be unknown, the contained immunoreceptor-tyrosine inhibitory motifs (ITIMs) and immunoreceptor-tyrosine activation motifs (ITAMs) are deemed to be involved in the regulation of the immune system	26402798	Details
TRD	polymorphism	N/A	PCR	MS	disease risk	We conclude there is no convincing evidence for an association of MS with TCR α, β, γ, and δ chain gene polymorphisms.	N/A	8857743	Details
HLA-DRB1	genotype	DR3	PCR	MS	Disease risk	There was no significant difference between any group of index cases and controls or affected females and male index cases or controls.	N/A	7853025	Details
HLA-DRB1	polymorphism	*07-*08	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
MEFV	polymorphisms	V726A	PCR	MS	Phenotypic risk	Our results indicate that MEFV gene mutations do not affect the neurologic prognosis in patients with MS.	N/A	24712487	Details
TAP2	Gene polymorphisms	TAP2 - 2155	PCR	MS	Disease risk	No significant differences in the frequencies of TAP polymorphisms were observed between both groups	These data suggest that TAP is not a susceptibility gene for MS	7929801	Details
FCRL3	SNP	rs2282284	PCR	Neuromyelitis optica (NMO)	Disease risk	Conclusions in the present study could be drawn that 4 SNPs in FCRL3 (FCRL3_3C, 5C, 6A, 8G) might account for increased risk of NMO in a Chinese-Han population. Nevertheless, further cohort studies are in demand to validate the association in the future	FCRL3 encoded a member of the immunoglobulin receptor superfamily, which could directly act against myelin-derived antigens.16 Furthermore, although the precise function of FCRL3 remains to be unknown, the contained immunoreceptor-tyrosine inhibitory motifs (ITIMs) and immunoreceptor-tyrosine activation motifs (ITAMs) are deemed to be involved in the regulation of the immune system	26402798	Details
HLA-DRB1	genotype	DR4	PCR	MS	Disease risk	There was no significant difference between any group of index cases and controls or affected females and male index cases or controls.	N/A	7853025	Details
HLA-DRB1	polymorphism	*0901	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
MEFV	polymorphisms	A744S	PCR	MS	Phenotypic risk	Our results indicate that MEFV gene mutations do not affect the neurologic prognosis in patients with MS.	N/A	24712487	Details
TNF	Gene polymorphisms	TNF - 376	PCR	MS	Disease risk	In MS， a statistically significant increase of A at position -376 in the TNFA gene was observed	The possibility that genetic susceptibility to MS might be influenced by TNF gene polymorphism has been repeatedly put forward	10522904	Details
FCRL3	SNP	rs2282283	PCR	Neuromyelitis optica (NMO)	Disease risk	Conclusions in the present study could be drawn that 4 SNPs in FCRL3 (FCRL3_3C, 5C, 6A, 8G) might account for increased risk of NMO in a Chinese-Han population. Nevertheless, further cohort studies are in demand to validate the association in the future	FCRL3 encoded a member of the immunoglobulin receptor superfamily, which could directly act against myelin-derived antigens.16 Furthermore, although the precise function of FCRL3 remains to be unknown, the contained immunoreceptor-tyrosine inhibitory motifs (ITIMs) and immunoreceptor-tyrosine activation motifs (ITAMs) are deemed to be involved in the regulation of the immune system	26402798	Details
HLA-DRB1	genotype	DR6	PCR	MS	Disease risk	There was no significant difference between any group of index cases and controls or affected females and male index cases or controls.	N/A	7853025	Details
HLA-DRB1	polymorphism	*1001	PCR	MS	Disease risk	Significant differences were detected between MS and control populations in the frequencies of DRB1*1501, DRB1*04, DQB1*0302, DQB1*0602, DQB1*0501, DQA1*0101, and DQA1*0103.	N/A	9328791	Details
MEFV	polymorphisms	R761H	PCR	MS	Phenotypic risk	Our results indicate that MEFV gene mutations do not affect the neurologic prognosis in patients with MS.	N/A	24712487	Details
TNF	Gene polymorphisms	TNF - 238	PCR	MS	Disease risk	whereas no significant differences were found with -238 and -308 genotype or allele frequencies	The possibility that genetic susceptibility to MS might be influenced by TNF gene polymorphism has been repeatedly put forward	10522904	Details
ESR1	Allele	NA	PCR	MS	Disease risk	Xba I gene polymorphisms in the ER α gene have correlation with MS and NMO. Xba I gene could be a risk factor of MS and NMO pathogenesis, especially the women with Xx genotype are more vulnerable.	T o study the polymorphism distribution of estrogen receptor (ER) α gene and the correlation between different types of polymorphism in multiple sclerosis (MS) and neuromyelitis optica (NMO) patients.	36254093	Details
APOE	SNP	N/A	PCR	MS	N/A	Later onset of chronic progressive MS was observed in patients carrying the epsilon2 allele, whereas APO E alleles were found at similar frequency in MS and in the control population.These findings indicate that clinical heterogeneity, but probably not susceptibility to the disease, is associated to APO E genotypes.	N/A	11109009	Details
CYP4F2	SNP	rs1558139	PCR	optic neuritis (ON)	Disease risk	The higher IL-17A levels were found to be associated with ON, while allele A at rs1558139 was associated only with ON with MS in male patients	In the central nervous system, IL-17A is associated with a wide range of neuropathological disorders (MS, epilepsy episodes of ischemic brain disorders). IL-17A, acting on spinal nerve roots and the spinal cord, contributes to neuropathic and inflammatory pain promotion through pain receptors.Also, IL-17A is very important to damaged sympathetic axons which innervate the cornea regeneration and growth.	29736281	Details
HLA-DRB1	genotype	DR7.1	PCR	MS	Disease risk	There was no significant difference between any group of index cases and controls or affected females and male index cases or controls.	N/A	7853025	Details
MEFV	polymorphisms	M680I (G/A)	PCR	MS	Phenotypic risk	Our results indicate that MEFV gene mutations do not affect the neurologic prognosis in patients with MS.	N/A	24712487	Details
TNF	Gene polymorphisms	TNF - 308	PCR	MS	Disease risk	whereas no significant differences were found with -238 and -308 genotype or allele frequencies	The possibility that genetic susceptibility to MS might be influenced by TNF gene polymorphism has been repeatedly put forward	10522904	Details
CCR5	Allele	NA	PCR	MS	Disease risk	These results suggest that the C C R5 d32 polymorphism is no t a major deter minant o f susceptibility to develop MS in the populatio n under study, and co nflict with a previo usly repo rted associatio n betw een C C R5 d32 carriage and a better prognosis	The C C R5 chemo kine recepto r has been implicated in the patho genesis of multiple sclerosis (MS). We carried out an allelic association study using a deletio n polymo rphism in the coding regio n o f the C C R5 gene in 331 relapsing/remitting (RR) and secondar y pro gressive (SP) MS patients, 108 primary pro gressive (PP) MS patients and 230 healthy controls.	15124759	Details
CD80	transitions,deletion	N/A	PCR	MS	N/A	We identified five genetic variants. None alter protein structure nor have apparent functional significance. Selected variants of sufficient frequency were tested for an association with course and severity of MS and one was tested for an association with susceptibility; none of the association tests were positive.	N/A	10742561	Details
HLA-DRB1	genotype	DR8	PCR	MS	Disease risk	There was no significant difference between any group of index cases and controls or affected females and male index cases or controls.	N/A	7853025	Details
CBLB	SNP	rs12487066	PCR	MS	Disease risk	The MS risk-related single nucleotide polymorphism of CBLB rs12487066 is associated with diminished CBL-B expression levels.	Mechanistically, the CBLB rs12487066 risk allele mediates increased binding of the transcription factor C/EBPb and reduced CBL-B expression in human CD4+ T cells.	25261476	Details
HPRT1	mutant frequency	N/A	PCR	MS	Phenotypic risk	In the chronic progressive group of MS, the mF increased over a 3-year period and appeared to correlate with the clinical worsening of the disease.	The reason for the discrepancy in the mF between the different clinical disease categories might relate to underlying differences in the tempo and nature of the autoimmune processes that sustain the disease.	8309581	Details
TNF	Gene polymorphisms	TNF - 238	PCR	MS	Disease risk	No significant differences regarding the TNF-alpha -238 and -308 polymorphisms were observed between MS patients and controls.	these differences could not be attributed to these promoter polymorphisms in our own study	10773851	Details
CD1A	Allele	NA	PCR	MS	Disease risk	CDIE 01-01 is associated with a reduced risk ofMS (OR 0.54, p=O.OOI); CDIA 02-02 (OR 1.99, p=0.012) or CDIE 02-02 (OR 2.45, p=O.OOO) with an increased risk.	Multiple sclerosis (MS) is thought to be an autoimmune T-cell-mediated disease directed at myelin antigens of the central nervous system.	21496400	Details
ERV3-1	six single base pair variations and a drop-out of a nucleotide	N/A	PCR	MS	N/A	Neither was there a significant difference in the distribution of the three alleles between MS patients with the progressive form and patients with relapsing/remitting MS. Our results are not in support of an association between ERV3 and MS.	N/A	8871766	Details
PSMB9	SNP	N/A	PCR	MS	N/A	We studied large multifunctional protease (LMP) 2 and 7 and transporter associated with antigen processing (TAP) 1 and 2 gene polymorphisms in 60 HLA-DRZ MS patients and 60 HLA-DR2 healthy subjects and found no specific or preferential RFLP patterns or coding sequence variants in the patient group.	N/A	7909590	Details
HLA-DRB1	genotype	DR7.2/9	PCR	MS	Disease risk	There was no significant difference between any group of index cases and controls or affected females and male index cases or controls.	N/A	7853025	Details
CBLB	SNP	rs2028597	PCR	MS	Disease risk	Interestingly, binding was predicted only for the C/EBPb binding site if it contained the risk (T) allele of rs12487066 , whereas the prediction for rs9657904 and rs2028597 showed no differential binding for C/EBPb.	N/A	25261476	Details
HLA-DRB1	polymorphisms	DRB1*15:01	PCR	MS	Disease risk	HLA-DRB1*15:01, 15:02 and DQB1*06:02 are the predisposing alleles while HLA-DRB1*14:04 is the protective allele for MS in our population.	N/A	33657520	Details
IL2RA	SNP	rs12722495	PCR	MS	Phenotypic risk	Here we use polychromatic flow cytometry to show that differences in surface expression of the human interleukin-2 (IL-2) receptor alpha (IL2RA, or CD25) protein are restricted to particular immune cell types and correlate with several haplotypes in the IL2RA region that have previously been associated with two autoimmune diseases, type 1 diabetes (T1D) and multiple sclerosis2–4.	N/A	19701192	Details
SYN3	SNP	g–196 (G > A)	PCR	MS	Disease risk	No significant difference was found in genotype and allele distribution for the g.–196 between patients and controls.	Synapsins are a family of abundant neuron-specific phosphoproteins, that have been recognised as playing crucial roles in synaptogenesis and neuronal plasticity, including regulation of synapse development, modulation of neurotransmitter release and formation of nerve terminals.	14991350	Details
TNF	Gene polymorphisms	TNF - 308	PCR	MS	Disease risk	No significant differences regarding the TNF-alpha -238 and -308 polymorphisms were observed between MS patients and controls.	these differences could not be attributed to these promoter polymorphisms in our own study	10773851	Details
CD1E	Allele	NA	PCR	MS	Disease risk	CDIE 01-01 is associated with a reduced risk ofMS (OR 0.54, p=O.OOI); CDIA 02-02 (OR 1.99, p=0.012) or CDIE 02-02 (OR 2.45, p=O.OOO) with an increased risk.	Multiple sclerosis (MS) is thought to be an autoimmune T-cell-mediated disease directed at myelin antigens of the central nervous system.	21496400	Details
PSMB8	SNP	N/A	PCR	MS	N/A	We studied large multifunctional protease (LMP) 2 and 7 and transporter associated with antigen processing (TAP) 1 and 2 gene polymorphisms in 60 HLA-DRZ MS patients and 60 HLA-DR2 healthy subjects and found no specific or preferential RFLP patterns or coding sequence variants in the patient group.	N/A	7909590	Details
HLA-DRB1	genotype	DR10	PCR	MS	Disease risk	There was no significant difference between any group of index cases and controls or affected females and male index cases or controls.	N/A	7853025	Details
CBLB	SNP	rs9657904	PCR	MS	Disease risk	Interestingly, binding was predicted only for the C/EBPb binding site if it contained the risk (T) allele of rs12487066 , whereas the prediction for rs9657904 and rs2028597 showed no differential binding for C/EBPb.	N/A	25261476	Details
HLA-DRB1	polymorphisms	DRB1*15:02	PCR	MS	Disease risk	HLA-DRB1*15:01, 15:02 and DQB1*06:02 are the predisposing alleles while HLA-DRB1*14:04 is the protective allele for MS in our population.	N/A	33657520	Details
IL2RA	SNP	rs2104286	PCR	MS	Phenotypic risk	Here we use polychromatic flow cytometry to show that differences in surface expression of the human interleukin-2 (IL-2) receptor alpha (IL2RA, or CD25) protein are restricted to particular immune cell types and correlate with several haplotypes in the IL2RA region that have previously been associated with two autoimmune diseases, type 1 diabetes (T1D) and multiple sclerosis2–4.	N/A	19701192	Details
SYN3	SNP	g–631 (C > G)	PCR	MS	Disease risk	A significant association with MS was observed for the g.–631 polymorphism.The C allele of the g.–631 polymorphism occurred less frequently in patients than in controls, and subjects who were carrying at least one C allele had a reduced risk of developing MS.The C allele of the g.–631C >G polymorphism was less frequent in the cases, and that individuals carrying the C allele were at reduced risk for developing MS.	Synapsins are a family of abundant neuron-specific phosphoproteins, that have been recognised as playing crucial roles in synaptogenesis and neuronal plasticity, including regulation of synapse development, modulation of neurotransmitter release and formation of nerve terminals.	14991350	Details
TNF	Alleles	a11	PCR	MS	Disease risk	Allele frequency for the a11 allele is in very significant association (P<0.0001) with MS	due in part to the association of the a11 allele with the HLA-DRB1*15 allele in patients	10773851	Details
CTLA4	Allele	NA	PCR	MS	Disease risk	Being homozygous for AT8 (common) allele of the 3V(514) microsatellite (OR: 1.69; CI: 0.99 – 2.86) and for the common 5V(318)*C/E1(49)*A/3V(514*AT8 haplotype (OR: 1.96; CI: 1.13 – 3.39) was associated with increased susceptibility to MS in Olmsted County.	We comprehensively screened CTLA4 for novel genetic variations in patients with MS.	12507781	Details
HLA-DPB1	polymorphism	N/A	PCR	MS	N/A	The distribution of the DPB1 alleles was not significantly different in multiple sclerosis patients and controls (p = 0.11).	The associations may be due to a pathogenic effect of the HLA antigens themselves or to linkage disequilibrium between the HLA genes and a closely located susceptibility gene.	1918327	Details
ABCB9	SNP	N/A	PCR	MS	N/A	We studied large multifunctional protease (LMP) 2 and 7 and transporter associated with antigen processing (TAP) 1 and 2 gene polymorphisms in 60 HLA-DRZ MS patients and 60 HLA-DR2 healthy subjects and found no specific or preferential RFLP patterns or coding sequence variants in the patient group.	N/A	7909590	Details
HLA-DRB1	genotype	DR11	PCR	MS	Disease risk	There was no significant difference between any group of index cases and controls or affected females and male index cases or controls.	N/A	7853025	Details
HLA-DRB1	SNP	rs3135005	PCR	MS	Disease risk	The presence of CCSVI was independent of HLA DRB1*1501 status in MS patients.	N/A	21340025	Details
HLA-DRB1	polymorphisms	DRB1*14:04	PCR	MS	Disease risk	HLA-DRB1*15:01, 15:02 and DQB1*06:02 are the predisposing alleles while HLA-DRB1*14:04 is the protective allele for MS in our population.	N/A	33657520	Details
SYN3	haplotype	C631 haplotype	PCR	MS	Disease risk	The distribution of haplotypes reported a significant difference between cases and controls with the C631 haplotype seeming to confer a significant protection against MS.	Synapsins are a family of abundant neuron-specific phosphoproteins, that have been recognised as playing crucial roles in synaptogenesis and neuronal plasticity, including regulation of synapse development, modulation of neurotransmitter release and formation of nerve terminals.	14991350	Details
MBP	Gene polymorphisms	a tetranucleotide (TGGA)n repeat polymorphism 5'	PCR	MS	Disease risk	Our results indicate that there is no association between MS and a polymorphism 5' to the MBP gene	We could not identify any significant difference in allele or genotype frequencies between MS patients and controls for the MBP alleles studied	7515903	Details
TAGAP	SNP	rs1738074	PCR	MS	Disease risk	The results suggested that TAGAP rs1738074 polymorphism could be considered as a risk factor in the prevalence of MS in the Iranian population	In the present study, the impact of rs1738074 single nucleotide polymorphism (SNP) in the TAGAP gene (TAGAP rs1738074) on the risk of MS was evaluated in a sample of the Iranian population.	28356229	Details
TRB	polymorphism	N/A	PCR	MS	N/A	For the autosomal recessive model with a penetrance range from 0.1 to 1.0, the LOD scores ranged from -8.20 to -32.98. These findings do not support a direct role of T-cell receptor beta-chain gene in the inheritance of MS.	N/A	1683213	Details
TAP2	SNP	N/A	PCR	MS	N/A	We studied large multifunctional protease (LMP) 2 and 7 and transporter associated with antigen processing (TAP) 1 and 2 gene polymorphisms in 60 HLA-DRZ MS patients and 60 HLA-DR2 healthy subjects and found no specific or preferential RFLP patterns or coding sequence variants in the patient group.	N/A	7909590	Details
HLA-DRB1	genotype	DR12	PCR	MS	Disease risk	There was no significant difference between any group of index cases and controls or affected females and male index cases or controls.	N/A	7853025	Details
HLA-DRB1	polymorphisms	DRB1*13:02	PCR	MS	Disease risk	Distribution of HLA-DRB1 allele carrier frequency in patients with MS and controls.	N/A	33657520	Details
SYN3	haplotype	A196 haplotype	PCR	MS	Disease risk	The distribution of haplotypes reported a significant difference between cases and controls with the A196 haplotype seeming to confer a significant protection against MS.	Synapsins are a family of abundant neuron-specific phosphoproteins, that have been recognised as playing crucial roles in synaptogenesis and neuronal plasticity, including regulation of synapse development, modulation of neurotransmitter release and formation of nerve terminals.	14991350	Details
BDNF	Allele	NA	PCR	MS	Disease risk	The BDNF-V al66Met-polymorphism leads to altered intracellular transport and secretion of BDNF, and is thus a logical candidate for a gene that influences susceptibility and, more specifically, the clinical course of multiple sclerosis.	Neurodegeneration following inflammatory injury is considered to be a pathological correlate of irreversible disability in patients with multiple sclerosis.	16046000	Details
TRB	SNP	Vβ5.2	PCR	MS	disease risk	The concurrent demonstration by others that T cells within demyelinating areas of multiple sclerosis brains preferentially express VP5.2 and V.86.1 suggests that the BP-specific clones derived from blood may be relevant to disease pathogenesis.	peripheral blood T cells are a reflection of cells involved in the central nervous system damage and that BP reactivity is a component of the pathogenic response in MS.	1717998	Details
HLA-DRB1	genotype	DR15	PCR	MS	Disease risk	There was no significant difference between any group of index cases and controls or affected females and male index cases or controls.	N/A	7853025	Details
HLA-DRB1	polymorphisms	DRB1*13:01	PCR	MS	Disease risk	Distribution of HLA-DRB1 allele carrier frequency in patients with MS and controls.	N/A	33657520	Details
HLA-DRB1	allele	DRB1*0901	PCR	MS	Disease risk	All patients with MS showed a significant decrease in the frequency of the DRB1*0901 allele compared with healthy controls.The DRB1*0901 allele was negatively associated with the absence of Barkhof brain lesions.	N/A	18952831	Details
HLA-DRB1	SNP	rs3135388	PCR	MS	Phenotypic risk	Carriership of HLA-DRB1*1501 (via rs3135388) was associated with the extent of focal ab-normalities in the spinal cord. Spinal cord lesions might be an explanation for increased MS disease severity in patients carrying HLA-DRB1*1501.	Multiple sclerosis (MS) is a heteroge-neous neurologic disease with extensive variation with respect to the most affected central nervous system re-gion (brain vs spinal cord).	20008659	Details
TRB	SNP	Vβ6.1	PCR	MS	disease risk	The concurrent demonstration by others that T cells within demyelinating areas of multiple sclerosis brains preferentially express VP5.2 and V.86.1 suggests that the BP-specific clones derived from blood may be relevant to disease pathogenesis.	peripheral blood T cells are a reflection of cells involved in the central nervous system damage and that BP reactivity is a component of the pathogenic response in MS.	1717998	Details
HLA-DRB1	allele	DR1	PCR	MS	Disease risk	HLA-DR, HLA-B, and HLA-A allele frequencies in Norwegian multiple sclerosis (MS) cases and controls	N/A	14989713	Details
HLA-DRB1	polymorphisms	DRB1*12:01	PCR	MS	Disease risk	Distribution of HLA-DRB1 allele carrier frequency in patients with MS and controls.	N/A	33657520	Details
HLA-DRB1	allele	DRB1*1501	PCR	MS	Disease risk	The frequency of the DRB1*1501 allele was insignificantly increased in the Barkhof brain lesion–positive group.	N/A	18952831	Details
CIITA	SNP	rs4774C	PCR	MS	Disease risk	This study has verified previous results about the strong gene–envi-ronment interaction between HHV6A active replication and MHC2TA rs4774C.Furthermore, a different clinical behavior for MS patients with HHV-6A active infection and minor allele C was found.	In a previous report, a strong gene–environment interaction between human herpesvirus 6A (HHV6A) active replication and MHC2TA rs4774C was demonstrated.	19659749	Details
P2RX7	SNP	rs1718119	PCR	MS	Disease risk	Although being preliminary and needing confirmation in an ampler cohort, these results suggest that 348Thr and 464Arg variants have a role as modulators of disease severity in RRMS patients.	N/A	36499708	Details
HLA-DRB1	allele	DR3	PCR	MS	Disease risk	HLA-DR, HLA-B, and HLA-A allele frequencies in Norwegian multiple sclerosis (MS) cases and controls	N/A	14989713	Details
HLA-DRB1	polymorphisms	DRB1*11:01	PCR	MS	Disease risk	Distribution of HLA-DRB1 allele carrier frequency in patients with MS and controls.	N/A	33657520	Details
HLA-DPB1	allele	DPB1*0501	PCR	MS	Disease risk	None of the DPB1 alleles differed significantly among groups.	N/A	18952831	Details
HLA-DRB1	SNP	DRB1*14 -	PCR	MS	Disease risk	HLA-DRB1*14-, HLA-DRB1*11-, HLA-DRB1*01-, and HLA-DRB1*10-bearing haplotypes are protective overall but they appear to operate by different mechanisms.	geography	17845076	Details
HLA-B	Allele	NA	PCR	MS	Disease risk	Carriage of the ligand of the inhibitory KIR3DL1 receptor, HLA-Bw4, was found to protect against MS in an HLA-DRB1 independent manner	Multiple sclerosis (MS) is a chronic inflammatory disease affecting the central nervous system. A human leukocyte antigen (HLA) class II association is well established (DRB1*1501-DQB1*0602), but more recently HLA class II–independent associations with HLA class I variants have also been reported.	19630074	Details
P2RX7	SNP	rs22390912	PCR	MS	Disease risk	Although being preliminary and needing confirmation in an ampler cohort, these results suggest that 348Thr and 464Arg variants have a role as modulators of disease severity in RRMS patients.	N/A	36499708	Details
CD3G	N/A	rs3753058	PCR	MS	Disease risk	Heterozygosity (HZ) in 4000 controls	Genes that control T cell activation downstream of the initial presentation of peptide antigen by HLA molecules may be regarded as prime candidate susceptibility genes in T cell mediated autoimmune diseases, such as MS	16764945	Details
HLA-DRB1	allele	DR4	PCR	MS	Disease risk	HLA-DR, HLA-B, and HLA-A allele frequencies in Norwegian multiple sclerosis (MS) cases and controls	N/A	14989713	Details
HLA-DRB1	polymorphisms	DRB1*10:01	PCR	MS	Disease risk	Distribution of HLA-DRB1 allele carrier frequency in patients with MS and controls.	N/A	33657520	Details
CCR5	polymorphism, allele	N/A	PCR	MS	Disease risk	The CCR5 phenotype, allele, and genotype frequencies for the study groups of unrelated MS patients and healthy controls did not differ significantly between 219 patients with MS and 354 control individuals.	N/A	12451219	Details
HLA-DRB1	SNP	DRB1*11 -	PCR	MS	Disease risk	HLA-DRB1*14-, HLA-DRB1*11-, HLA-DRB1*01-, and HLA-DRB1*10-bearing haplotypes are protective overall but they appear to operate by different mechanisms.	geography	17845076	Details
STAT3	SNP	rs744166	PCR	MS	Disease risk	observed a nominally significant, albeit weak association between rs744166 and MS susceptibility (odds ratio=1.09, P=0.012) in our sample	Recent genome-wide association studies have implicated the “signal transducer and activator of transcription 3” gene (STAT3) as a putative new multiple sclerosis (MS) susceptibility locus.	22095036	Details
CD44	N/A	rs1058200	PCR	MS	Disease risk	Heterozygosity (HZ) in 4000 controls	Genes that control T cell activation downstream of the initial presentation of peptide antigen by HLA molecules may be regarded as prime candidate susceptibility genes in T cell mediated autoimmune diseases, such as MS	16764945	Details
HLA-DRB1	allele	DR7	PCR	MS	Disease risk	HLA-DR, HLA-B, and HLA-A allele frequencies in Norwegian multiple sclerosis (MS) cases and controls	N/A	14989713	Details
HLA-DRB1	polymorphisms	DRB1*08:03:02	PCR	MS	Disease risk	Distribution of HLA-DRB1 allele carrier frequency in patients with MS and controls.	N/A	33657520	Details
Val158Met	polymorphism	rs4680 Val158Met (Val/Val, Val/Met,and Met/Met)	PCR	MS	Disease risk	Distribution of rs4680 Val158Met genotypes was not significantly different between individuals with MS in general and healthy people.	N/A	24290452	Details
HLA-DRB1	SNP	DRB1*01 -	PCR	MS	Disease risk	HLA-DRB1*14-, HLA-DRB1*11-, HLA-DRB1*01-, and HLA-DRB1*10-bearing haplotypes are protective overall but they appear to operate by different mechanisms.	in the presence of HLA-DRB1*15, showing a clear protective effect in the presence of HLA-DRB1*15	17845076	Details
STAT3	SNP	rs2293152	PCR	MS	Disease risk	observed a nominally significant, albeit weak association between rs744166 and MS susceptibility (odds ratio=1.09, P=0.012) in our sample	Recent genome-wide association studies have implicated the “signal transducer and activator of transcription 3” gene (STAT3) as a putative new multiple sclerosis (MS) susceptibility locus.	22095036	Details
CD44	N/A	rs1467558	PCR	MS	Disease risk	Heterozygosity (HZ) in 4000 controls	Genes that control T cell activation downstream of the initial presentation of peptide antigen by HLA molecules may be regarded as prime candidate susceptibility genes in T cell mediated autoimmune diseases, such as MS	16764945	Details
HLA-DRB1	allele	DR8	PCR	MS	Disease risk	HLA-DR, HLA-B, and HLA-A allele frequencies in Norwegian multiple sclerosis (MS) cases and controls	N/A	14989713	Details
HLA-DRB1	polymorphisms	DRB1*07:01:01	PCR	MS	Disease risk	Distribution of HLA-DRB1 allele carrier frequency in patients with MS and controls.	N/A	33657520	Details
HLA-DRB1	allele	N/A	PCR	MS	Disease risk	A transmission disequilibrium test analysis was significant for the DRB1*15 allele within this single family.	The inheritance pattern in this family suggests the presence of a single major locus responsible for multiple sclerosis susceptibility,with DBR1 acting as an important modifier.	12076998	Details
Val158Met	polymorphism	rs4680 Val158Met (Val/Val, Val/Met,and Met/Met)	PCR	MS	Phenotypic risk	This study suggests that the Val158Met polymorphism is associated with the presence of pain in MS, because the presence of the Met/Met genotype was more prevalent in those patients with pain.	The catechol-Omethyltransferase (COMT) gene is one of the several potential genetic determinants of nociceptive modulation.Genetic polymorphism due to a G/A substitution at codon 158 of the COMT gene, leading to a Val to Met substitution, results in gene activity differences.The presence of a Met allele results in low enzymatic activity.	24290452	Details
HLA-DRB1	SNP	DRB1*10 -	PCR	MS	Disease risk	HLA-DRB1*14-, HLA-DRB1*11-, HLA-DRB1*01-, and HLA-DRB1*10-bearing haplotypes are protective overall but they appear to operate by different mechanisms.	in the presence of HLA-DRB1*15, showing a clear protective effect in the presence of HLA-DRB1*15	17845076	Details
TNFRSF1A	SNP	Rs4149584	PCR	MS	Disease risk	Clinical characteristics of childhood MS patients with or without mutations did not differ significantly. Conclusion One third of our childhood MS patients had a heterozygous mutation in the TNFRSF1A and/or MEFV gene.	To investigate frequency and phenotype of TNFRSF1A and MEFV mutations in childhood-onset multiple sclerosis (MS).	28927886	Details
CD5	N/A	rs637186	PCR	MS	Disease risk	Heterozygosity (HZ) in 4000 controls	Genes that control T cell activation downstream of the initial presentation of peptide antigen by HLA molecules may be regarded as prime candidate susceptibility genes in T cell mediated autoimmune diseases, such as MS	16764945	Details
HLA-DRB1	allele	DR11	PCR	MS	Disease risk	HLA-DR, HLA-B, and HLA-A allele frequencies in Norwegian multiple sclerosis (MS) cases and controls	N/A	14989713	Details
HLA-DRB1	polymorphisms	DRB1*04:03:01	PCR	MS	Disease risk	Distribution of HLA-DRB1 allele carrier frequency in patients with MS and controls.	N/A	33657520	Details
Eae2	N/A	N/A	PCR	EAE	Phenotypic risk	In the present study we find one region on chromosome 7,not previously identified in this strain combination,that affects the disease at significant logarithm of the odds score and six regions showing suggestive evidence for linkage to disease phenotypse.	N/A	11751775	Details
IL1A	polymorphism	-889 C/T	PCR	MS	Disease risk	In the case of the IL-1A polymorphism, the gene frequency of 91 benign was not statistically diVerent from those of the 107 non-benign patients with multiple sclerosis.IL-1A seemed to aVect the distribution of the age at multiple sclerosis onset.	N/A	11183041	Details
HLA-DRB1	SNP	DRB1*15 -	PCR	MS	Disease risk	We confirm that HLA-DRB1*15- and HLA-DRB1*17-bearing haplotypes increase risk of MS	and is in keeping with an additive mode of inheritance for HLA-DRB1*15, similar to other studies	17845076	Details
CD5	N/A	rs2241002	PCR	MS	Disease risk	Heterozygosity (HZ) in 4000 controls	Genes that control T cell activation downstream of the initial presentation of peptide antigen by HLA molecules may be regarded as prime candidate susceptibility genes in T cell mediated autoimmune diseases, such as MS	16764945	Details
HLA-DRB1	allele	DR13	PCR	MS	Disease risk	HLA-DR, HLA-B, and HLA-A allele frequencies in Norwegian multiple sclerosis (MS) cases and controls	N/A	14989713	Details
HLA-DRB1	polymorphisms	DRB1*04:01:01	PCR	MS	Disease risk	Distribution of HLA-DRB1 allele carrier frequency in patients with MS and controls.	N/A	33657520	Details
IL4	allele	variable number of tandem repeat polymorphism	PCR	MS	Disease risk	Our results show that the IL-4 B1 allele is associated with late onset of MS and therefore might represent a modifier of age of onset rather than a susceptibility factor for patients with MS.	N/A	9184650	Details
IL1B	polymorphism	-511 C/T	PCR	MS	Disease risk	As for the IL-1B polymorphism, the gene frequency of the 73 benign patients was also similar to those of the 82 non benign patients with multiple sclerosis. IL-1B genotypes seemed to aVect the distribution of the age at multiple sclerosis onset.	N/A	11183041	Details
HLA-DRB1	SNP	DRB1*17 -	PCR	MS	Disease risk	We confirm that HLA-DRB1*15- and HLA-DRB1*17-bearing haplotypes increase risk of MS	In this Canadian sample, HLA-DRB1*17 haplotypes act in an additive fashion	17845076	Details
CD14	Allele	NA	PCR	MS	Disease risk	CD14 polymorphism frequency between the healthy controls and the MS patients were not significantly differ-ent.	Soluble (s) CD14, being a receptor for lipopolysaccharides (LPSs) may inhibit LPS-triggered apoptosis and T lym-phocyte proliferation	22703766	Details
CD69	N/A	rs3176798	PCR	MS	Disease risk	Heterozygosity (HZ) in 4000 controls	Genes that control T cell activation downstream of the initial presentation of peptide antigen by HLA molecules may be regarded as prime candidate susceptibility genes in T cell mediated autoimmune diseases, such as MS	16764945	Details
MEFV	mutation	M694V	PCR	MS	Disease risk	non-Asheknazi MS patients carrying one mutated MEFV gene, particularly M694V, expressed rapid progression to disability.	The expressed mutation may increase inflammatory damage inflicted by autoimmune responses.	12700594	Details
HLA-DRB1	allele	DR15	PCR	MS	Disease risk	HLA-DR, HLA-B, and HLA-A allele frequencies in Norwegian multiple sclerosis (MS) cases and controls	N/A	14989713	Details
HLA-DRB1	polymorphisms	DRB1*03:01:01	PCR	MS	Disease risk	Distribution of HLA-DRB1 allele carrier frequency in patients with MS and controls.	N/A	33657520	Details
CD14	Allele	NA	PCR	MS	Disease risk	CD14 polymorphism frequency between the healthy controls and the MS patients were not significantly differ-ent.	Soluble (s) CD14, being a receptor for lipopolysaccharides (LPSs) may inhibit LPS-triggered apoptosis and T lym-phocyte proliferation	22703766	Details
PLCG1	N/A	rs753381	PCR	MS	Disease risk	Heterozygosity (HZ) in 4000 controls	Genes that control T cell activation downstream of the initial presentation of peptide antigen by HLA molecules may be regarded as prime candidate susceptibility genes in T cell mediated autoimmune diseases, such as MS	16764945	Details
MEFV	mutation	V726A	PCR	MS	Disease risk	non-Asheknazi MS patients carrying one mutated MEFV gene, particularly M694V, expressed rapid progression to disability.	The expressed mutation may increase inflammatory damage inflicted by autoimmune responses.	12700594	Details
HLA-B	allele	B7	PCR	MS	Disease risk	HLA-DR, HLA-B, and HLA-A allele frequencies in Norwegian multiple sclerosis (MS) cases and controls	N/A	14989713	Details
HLA-DRB1	polymorphisms	DRB1*01:01:01	PCR	MS	Disease risk	Distribution of HLA-DRB1 allele carrier frequency in patients with MS and controls.	N/A	33657520	Details
NOTCH4	Allele	NA	PCR	MS	Disease risk	We conclude that alleles of the NOTCH4 and TNFa genes are unlikely to be of importance for the susceptibility to MS, although specific alleles of these genes are often carried on the same haplotype as DR15, DQ6.	N/A	14651518	Details
PLCG1	N/A	rs8192707	PCR	MS	Disease risk	Heterozygosity (HZ) in 4000 controls	Genes that control T cell activation downstream of the initial presentation of peptide antigen by HLA molecules may be regarded as prime candidate susceptibility genes in T cell mediated autoimmune diseases, such as MS	16764945	Details
MEFV	mutation	E148Q	PCR	MS	Disease risk	non-Asheknazi MS patients carrying one mutated MEFV gene, particularly M694V, expressed rapid progression to disability.	The expressed mutation may increase inflammatory damage inflicted by autoimmune responses.	12700594	Details
HLA-B	allele	B8	PCR	MS	Disease risk	HLA-DR, HLA-B, and HLA-A allele frequencies in Norwegian multiple sclerosis (MS) cases and controls	N/A	14989713	Details
HLA-DQB1	polymorphisms	DQB1*02:01	PCR	MS	Disease risk	Distribution of HLA-DQB1 allele carrier frequency in patients with MS and controls.	N/A	33657520	Details
CNTF	SNP	the G-to-A CNTF null mutation at position -6 of the second exon(CNTF -/-)	PCR	MS	Disease risk	The homozygous CNTF null mutation (CNTF -/-) was found in 7 of the 288 randomly selected patients with MS. Patients with the CNTF -/- genotype had a significantly earlier onset of disease with predominant motor symptoms.CNTF contributes to time and site of early clinical manifestation. The frequency of patients with MS with a homozygous CNTF null mutation in this population was not higher than in control groups, indicating that the CNTF null mutation is not a risk factor for development of MS.	Immune-mediated demyelination and axonal damage lead to early functional impairment in multiple sclerosis (MS). Ciliary neurotrophic factor (CNTF) is a potent survival factor for neurons and oligodendrocytes and may be relevant in reducing tissue destruction during inflammatory attacks.	11890844	Details
HLA-DQB1	Gene polymorphisms	G511525 and D6S1666	PCR	MS	Disease risk	The twolocus genotype association analysis showed that in individuals who carry only one of the risk haplotypes the risk for MS is moderately increased (odds ratio (OR) 2.82; 95% confidence interval (CI) 1.50–5.31). However, in individuals carrying two risk haplotypes the risk for MS is highly increased compared with individuals who carry no risk haplotypes (OR 37.00; 95% CI 8.31–164.74).	follow an intermediate mode of inheritance	25671658	Details
TNF	Allele	NA	PCR	MS	Disease risk	We conclude that alleles of the NOTCH4 and TNFa genes are unlikely to be of importance for the susceptibility to MS, although specific alleles of these genes are often carried on the same haplotype as DR15, DQ6.	N/A	14651518	Details
PTPN12	N/A	rs9640663	PCR	MS	Disease risk	Heterozygosity (HZ) in 4000 controls	Genes that control T cell activation downstream of the initial presentation of peptide antigen by HLA molecules may be regarded as prime candidate susceptibility genes in T cell mediated autoimmune diseases, such as MS	16764945	Details
MEFV	mutation	K695R	PCR	MS	Disease risk	non-Asheknazi MS patients carrying one mutated MEFV gene, particularly M694V, expressed rapid progression to disability.	The expressed mutation may increase inflammatory damage inflicted by autoimmune responses.	12700594	Details
HLA-B	allele	B12	PCR	MS	Disease risk	HLA-DR, HLA-B, and HLA-A allele frequencies in Norwegian multiple sclerosis (MS) cases and controls	N/A	14989713	Details
HLA-DQB1	polymorphisms	DQB1*03:01	PCR	MS	Disease risk	Distribution of HLA-DQB1 allele carrier frequency in patients with MS and controls.	N/A	33657520	Details
ACE	Gene polymorphisms	ACE I/D	PCR	MS	Disease risk	For ACE I/D polymorphism, neither significant differences in the genotype–phenotype study nor in the case– control study were observed	N/A	21320707	Details
PRRC2A	SNP	rs2242659	PCR	MS	Disease risk	Genotype AT of rs2844470 and AG of rs2242659 increased risk susceptibility for AQP4+ NMOSD and MS	The identified PRRC2A variants may shed light on the pathogenesis of NMOSD and MS and potentially lead to an individualized therapeutic approach for both distinct disease entities	32862241	Details
HLA-DRB1	Allele	NA	PCR	MS	Disease risk	HLA-DRB1*15 was found to be associated with multiple sclerosis in the Lithu-anian population.	The aim of the present study was to investigate the influence of HLA-DRB1 alleles on the genetic susceptibility to multiple sclerosis in the Lithuanian population.	22370504	Details
PTPN12	N/A	rs3750050	PCR	MS	Disease risk	Heterozygosity (HZ) in 4000 controls	Genes that control T cell activation downstream of the initial presentation of peptide antigen by HLA molecules may be regarded as prime candidate susceptibility genes in T cell mediated autoimmune diseases, such as MS	16764945	Details
HLA-B	allele	B15	PCR	MS	Disease risk	HLA-DR, HLA-B, and HLA-A allele frequencies in Norwegian multiple sclerosis (MS) cases and controls	N/A	14989713	Details
HLA-DQB1	polymorphisms	DQB1*03:02	PCR	MS	Disease risk	Distribution of HLA-DQB1 allele carrier frequency in patients with MS and controls.	N/A	33657520	Details
ACE	Gene polymorphisms	ATG M235T	PCR	MS	Disease risk	No significant association with susceptibility was observed.	N/A	21320707	Details
PRRC2A	SNP	rs2844470	PCR	MS	Disease risk	Genotype AT of rs2844470 and AG of rs2242659 increased risk susceptibility for AQP4+ NMOSD and MS	The identified PRRC2A variants may shed light on the pathogenesis of NMOSD and MS and potentially lead to an individualized therapeutic approach for both distinct disease entities	32862241	Details
HLA-DRB1	Allele	NA	PCR	MS	Disease risk	We confirm, primarily in the cohort originating from Continental Spain, that similar to other high-risk groups, there was a significant association with HLA-DR2	The HLA-DR2 haplotype (DRB1 * 1501, DQB1 * 0602) on chromosome 6p21 has consistently demonstrated both association and linkage with multiple sclerosis (MS) in case-control and family studies, particularly in Caucasians of Northern European descent.	12225902	Details
PTPN3	N/A	rs101168060	PCR	MS	Disease risk	Heterozygosity (HZ) in 4000 controls	Genes that control T cell activation downstream of the initial presentation of peptide antigen by HLA molecules may be regarded as prime candidate susceptibility genes in T cell mediated autoimmune diseases, such as MS	16764945	Details
HLA-B	allele	B27	PCR	MS	Disease risk	HLA-DR, HLA-B, and HLA-A allele frequencies in Norwegian multiple sclerosis (MS) cases and controls	N/A	14989713	Details
HLA-DQB1	polymorphisms	DQB1*03:03	PCR	MS	Disease risk	Distribution of HLA-DQB1 allele carrier frequency in patients with MS and controls.	N/A	33657520	Details
Eae5	N/A	N/A	PCR	EAE	Phenotypic risk	Pia4: severity, DA additive (8.4)	N/A	10640775	Details
NOS1	allele	N/A	PCR	MS	Disease risk	In this Australian population,13 alleles of this polymorphism were identified. This analysis indicates that the nNOS variant does not confer an altered effect on MS. Rank analysis also indicated that allelic distributions were not significantly different between test groups. Stratified analyses testing for a gender-specific relationship between MS and nNOS and comparisons of a specific clinical course group were also negative for association.	Nitric oxide (NO) production arising from nNOS has been involved in the pathophysiology of several disorders of the brain.NO has been shown to be toxic to oligodendrocytes and to induce axonal degeneration.Nitric oxide is also known to be a modulator of neuronal function affecting the release of neurotransmitters.	14759629	Details
ACE	Gene polymorphisms	ATG (6)A/G	PCR	MS	Disease risk	No significant association with susceptibility was observed.	N/A	21320707	Details
PRRC2A	SNP	rs2736157	PCR	MS	Disease risk	we identified various gene expression levels in disease-related regions that are significantly modulated by three cis-eQTL SNPs rs2736157, rs2736171 and rs2242659	The identified PRRC2A variants may shed light on the pathogenesis of NMOSD and MS and potentially lead to an individualized therapeutic approach for both distinct disease entities	32862241	Details
PTPN6	N/A	rs2301262	PCR	MS	Disease risk	Heterozygosity (HZ) in 4000 controls	Genes that control T cell activation downstream of the initial presentation of peptide antigen by HLA molecules may be regarded as prime candidate susceptibility genes in T cell mediated autoimmune diseases, such as MS	16764945	Details
HLA-B	allele	B35	PCR	MS	Disease risk	HLA-DR, HLA-B, and HLA-A allele frequencies in Norwegian multiple sclerosis (MS) cases and controls	N/A	14989713	Details
HLA-DQB1	polymorphisms	DQB1*04:01	PCR	MS	Disease risk	Distribution of HLA-DQB1 allele carrier frequency in patients with MS and controls.	N/A	33657520	Details
Eae10	N/A	N/A	PCR	EAE	Phenotypic risk	Pia6: chronicity, DA recessive (4.9)	N/A	10640775	Details
APOE	SNP	rs7412 (C/T)	PCR	MS	Disease risk	Hierarchical linear regression analyses suggested that after controlling for demographics, disease duration, and disability, ApoE ε2 significantly predicted increased positive affect (R2Δ = 0.05, F(1,94) = 5.44, P = 0.02) and was associated with decreased severity of depressive symptoms, although this did not reach statistical significance (R2Δ = 0.03, F(1,94) = 3.44, P = 0.06). ApoE ε4 did not significantly predict depression status.	N/A	19244396	Details
PRRC2A	SNP	rs2736171	PCR	MS	Disease risk	we identified various gene expression levels in disease-related regions that are significantly modulated by three cis-eQTL SNPs rs2736157, rs2736171 and rs2242659	The identified PRRC2A variants may shed light on the pathogenesis of NMOSD and MS and potentially lead to an individualized therapeutic approach for both distinct disease entities	32862241	Details
CBS	c.844_855ins68bp	N/A	PCR	MS	Disease risk	Conclusively, mutant variants of CBS and RFC1 may be associated with the age of RRMS onset.	N/A	24412677	Details
SLAMF1	N/A	rs164288	PCR	MS	Disease risk	Heterozygosity (HZ) in 4000 controls	Genes that control T cell activation downstream of the initial presentation of peptide antigen by HLA molecules may be regarded as prime candidate susceptibility genes in T cell mediated autoimmune diseases, such as MS	16764945	Details
HLA-B	allele	B40	PCR	MS	Disease risk	HLA-DR, HLA-B, and HLA-A allele frequencies in Norwegian multiple sclerosis (MS) cases and controls	N/A	14989713	Details
HLA-DQB1	polymorphisms	DQB1*05:01	PCR	MS	Disease risk	Distribution of HLA-DQB1 allele carrier frequency in patients with MS and controls.	N/A	33657520	Details
Eae1	N/A	N/A	PCR	EAE	Phenotypic risk	Pia1: severity/chronicity, DA dominant (3.0)	N/A	10640775	Details
APOE	SNP	rs429358 (C/T)	PCR	MS	Disease risk	Hierarchical linear regression analyses suggested that after controlling for demographics, disease duration, and disability, ApoE ε2 significantly predicted increased positive affect (R2Δ = 0.05, F(1,94) = 5.44, P = 0.02) and was associated with decreased severity of depressive symptoms, although this did not reach statistical significance (R2Δ = 0.03, F(1,94) = 3.44, P = 0.06). ApoE ε4 did not significantly predict depression status.	N/A	19244396	Details
CD58	SNP	rs2300747	PCR	MS	Disease risk	We also confirmed higher frequency of A and C alleles in rs2300747 and rs12044852 of CD58 gene and G allele in rs929230 of CD6 gene in MS as compared to controls	N/A	36451826	Details
RFC1	c.80G>A	N/A	PCR	MS	Disease risk	Conclusively, mutant variants of CBS and RFC1 may be associated with the age of RRMS onset.	N/A	24412677	Details
SLAMF1	N/A	rs3796504	PCR	MS	Disease risk	Heterozygosity (HZ) in 4000 controls	Genes that control T cell activation downstream of the initial presentation of peptide antigen by HLA molecules may be regarded as prime candidate susceptibility genes in T cell mediated autoimmune diseases, such as MS	16764945	Details
HLA-A	allele	A1	PCR	MS	Disease risk	HLA-DR, HLA-B, and HLA-A allele frequencies in Norwegian multiple sclerosis (MS) cases and controls	N/A	14989713	Details
HLA-DQB1	polymorphisms	DQB1*06:01	PCR	MS	Disease risk	Distribution of HLA-DQB1 allele carrier frequency in patients with MS and controls.	N/A	33657520	Details
Eae44b	N/A	N/A	PCR	EAE	Phenotypic risk	Piax (suggestive): severity, DA recessive (3.2)	N/A	10640775	Details
CD58	SNP	rs12044852	PCR	MS	Disease risk	We also confirmed higher frequency of A and C alleles in rs2300747 and rs12044852 of CD58 gene and G allele in rs929230 of CD6 gene in MS as compared to controls	N/A	36451826	Details
GRIN1	SNP	rs4880213	PCR	MS	Disease risk	The C allele of rs4880213 was found to be associated with reduced NMDAR-mediated cortical excitability, and with increased probability of having more disability than the CT/TT MS subjects.	Signaling through glutamate NMDARs enhances both compensatory synaptic plasticity and excitotoxic neurodegeneration, impacting in opposite ways on RR-MS and PP-MS pathophysiological mechanisms.	23840674	Details
SLAMF1	N/A	rs2295612	PCR	MS	Disease risk	Heterozygosity (HZ) in 4000 controls	Genes that control T cell activation downstream of the initial presentation of peptide antigen by HLA molecules may be regarded as prime candidate susceptibility genes in T cell mediated autoimmune diseases, such as MS	16764945	Details
TLR4	mutation	Asp299Gly	PCR	MS	Phenotype risk	In vitro LPS stimulation studies showed a significantly lower proliferation of PBMCs from donors heterozygous for the Asp299Gly mutation in comparison to PBMCs from individuals with the wild-type genotype ( p = 0.01).	It is possible that the reduced activity towards activation via the TLR-4 pathway takes place on both activating and suppressing cell types which then leads to a new equilibrium with the net result of a normal overall function.	15932772	Details
HLA-A	allele	A2	PCR	MS	Disease risk	HLA-DR, HLA-B, and HLA-A allele frequencies in Norwegian multiple sclerosis (MS) cases and controls	N/A	14989713	Details
HLA-DQB1	polymorphisms	DQB1*06:02	PCR	MS	Disease risk	HLA-DRB1*15:01, 15:02 and DQB1*06:02 are the predisposing alleles while HLA-DRB1*14:04 is the protective allele for MS in our population.	N/A	33657520	Details
Eae11	N/A	N/A	PCR	EAE	Disease risk	Pia2: onset, E3 dominant (3.9)	N/A	10640775	Details
CD6	SNP	rs929230	PCR	MS	Disease risk	We also confirmed higher frequency of A and C alleles in rs2300747 and rs12044852 of CD58 gene and G allele in rs929230 of CD6 gene in MS as compared to controls	N/A	36451826	Details
PTPN22	N/A	rs2476601	PCR	MS	Disease risk	Heterozygosity (HZ) in 4000 controls	Genes that control T cell activation downstream of the initial presentation of peptide antigen by HLA molecules may be regarded as prime candidate susceptibility genes in T cell mediated autoimmune diseases, such as MS	16764945	Details
TLR4	genotype	+896 A/A	PCR	MS	Phenotype risk	However, these functional changes seem not to have any impact on the clinical presentation of MS patients with different TLR-4 genotypes.	It is possible that the reduced activity towards activation via the TLR-4 pathway takes place on both activating and suppressing cell types which then leads to a new equilibrium with the net result of a normal overall function.	15932772	Details
HLA-A	allele	A3	PCR	MS	Disease risk	HLA-DR, HLA-B, and HLA-A allele frequencies in Norwegian multiple sclerosis (MS) cases and controls	N/A	14989713	Details
HLA-DQB1	polymorphisms	DQB1*06:09	PCR	MS	Disease risk	Distribution of HLA-DQB1 allele carrier frequency in patients with MS and controls.	N/A	33657520	Details
IL10	N/A	IL-10G7-11	PCR	MS	Disease risk	No other allele showed a significant difference between patients and controls, and the TDT analysis yielded negative results.	N/A	12101075	Details
VDR	SNP	rs731236	PCR	MS	Disease risk	We found a positive association of the genetic VDR polymorphisms TaqI (rs731236) and BsmI (rs1544410), with the risk of MS in a sample of Mexican adults	Due the important immune-modulating properties of Vitamin D, Vitamin D receptor (VDR) gene polymorphisms - which interfere with the actions of Vitamin D- could be related to increased risk of MS.	28385183	Details
IL23A	SNP	rs2066808	PCR	MS	Disease risk	We conclude that variants in IL-23A and IL-23R genes were associated with the risk of MS or other IDD diseases.	Interleukin-23A (IL23A) regulates and coordinates the activities of immune cells by interacting with its receptor IL23R and plays key roles in the pathogenesis of immune inflammatory diseases.	27893410	Details
TGFB2	N/A	rs10495098	PCR	MS	Disease risk	Our failure to find an association between TGFB2 and MS is in keeping with the negative findings of two previous studies, although these were limited by their sample size and choice of only one microsatellite marker in the 5’ flanking region	The transforming growth factor betas (TGFbs) control the growth, differentiation and function of a wide range of cells and have been implicated in many different disease processes	17431704	Details
TLR4	genotype	+896 A/G	PCR	MS	Phenotype risk	However, these functional changes seem not to have any impact on the clinical presentation of MS patients with different TLR-4 genotypes.	It is possible that the reduced activity towards activation via the TLR-4 pathway takes place on both activating and suppressing cell types which then leads to a new equilibrium with the net result of a normal overall function.	15932772	Details
HLA-A	allele	A9	PCR	MS	Disease risk	HLA-DR, HLA-B, and HLA-A allele frequencies in Norwegian multiple sclerosis (MS) cases and controls	N/A	14989713	Details
HLA-DRB1	genotype	DRB1×01:01-DQB1×05:01	PCR	MS	Disease risk	Frequency distribution of the DRB1-DQB1 haplotypes in patients with MS and controls.	N/A	33657520	Details
IL10	allele	IL-10G13-15	PCR	MS	Disease risk	No other allele showed a significant difference between patients and controls, and the TDT analysis yielded negative results.	N/A	12101075	Details
VDR	SNP	rs1544410	PCR	MS	Disease risk	We found a positive association of the genetic VDR polymorphisms TaqI (rs731236) and BsmI (rs1544410), with the risk of MS in a sample of Mexican adults	Due the important immune-modulating properties of Vitamin D, Vitamin D receptor (VDR) gene polymorphisms - which interfere with the actions of Vitamin D- could be related to increased risk of MS.	28385183	Details
IL23A	SNP	rs2371494	PCR	MS	Disease risk	We conclude that variants in IL-23A and IL-23R genes were associated with the risk of MS or other IDD diseases.	Interleukin-23A (IL23A) regulates and coordinates the activities of immune cells by interacting with its receptor IL23R and plays key roles in the pathogenesis of immune inflammatory diseases.	27893410	Details
TGFB2	N/A	rs6658835	PCR	MS	Disease risk	suggesting that rs6658835*G may be the causative variant	The transforming growth factor betas (TGFbs) control the growth, differentiation and function of a wide range of cells and have been implicated in many different disease processes	17431704	Details
TLR4	genotype	+896 AG/G	PCR	MS	Phenotype risk	However, these functional changes seem not to have any impact on the clinical presentation of MS patients with different TLR-4 genotypes.	It is possible that the reduced activity towards activation via the TLR-4 pathway takes place on both activating and suppressing cell types which then leads to a new equilibrium with the net result of a normal overall function.	15932772	Details
HLA-A	allele	A10	PCR	MS	Disease risk	HLA-DR, HLA-B, and HLA-A allele frequencies in Norwegian multiple sclerosis (MS) cases and controls	N/A	14989713	Details
VDR	polymorphism	VDRG	PCR	MS	Disease risk	These results indicate that VDRG polymorphism may be associated with susceptibility to MS.	N/A	10967184	Details
LTA	polymorphisms	TNF-b*1	PCR	MS	Disease risk	However, the co-occurrence of HLA-DRB 1 * 15,16 and the TNF-b*2 allele gives rise to a slightly increased relative risk for MS(RR =5.39). No such increase was found for the DRB 1 *04 positive RA patients.	N/A	9098447	Details
HLA-DRB1	genotype	DRB1×03:01-DQB1×02:02	PCR	MS	Disease risk	Frequency distribution of the DRB1-DQB1 haplotypes in patients with MS and controls.	N/A	33657520	Details
IL10	allele	IL-10G12	PCR	MS	Disease risk	IL-10G12 allele was significantly increased in MS patients	N/A	12101075	Details
AGER	Gene polymorphisms	p.82G>S	PCR	MS	Disease risk	The present study provides preliminary evidence that the gain-of-function p.82G>S polymorphism in the RAGE gene is associated with an increased risk of MS in the Chinese population	The receptor for advanced glycation end products (RAGE) and its proinflammatory ligand, S100-calgranulins, are critically implicated in the pathological progression of multiple sclerosis	21511691	Details
IL23A	SNP	rs11575248	PCR	MS	Disease risk	We conclude that variants in IL-23A and IL-23R genes were associated with the risk of MS or other IDD diseases.	Interleukin-23A (IL23A) regulates and coordinates the activities of immune cells by interacting with its receptor IL23R and plays key roles in the pathogenesis of immune inflammatory diseases.	27893410	Details
TGFB2	N/A	rs4846476	PCR	MS	Disease risk	Our failure to find an association between TGFB2 and MS is in keeping with the negative findings of two previous studies, although these were limited by their sample size and choice of only one microsatellite marker in the 5’ flanking region	The transforming growth factor betas (TGFbs) control the growth, differentiation and function of a wide range of cells and have been implicated in many different disease processes	17431704	Details
HLA-DRB1	polymorphisms	DRB1*01	PCR	MS	Phenotype risk	The other alleles did not show differences.	N/A	21418440	Details
HLA-A	allele	A11	PCR	MS	Disease risk	HLA-DR, HLA-B, and HLA-A allele frequencies in Norwegian multiple sclerosis (MS) cases and controls	N/A	14989713	Details
HLA-DRB1	polymorphism	DRB1*1501	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
LTA	polymorphisms	TNF-b*2	PCR	MS	Disease risk	However, the co-occurrence of HLA-DRB 1 * 15,16 and the TNF-b*2 allele gives rise to a slightly increased relative risk for MS(RR =5.39). No such increase was found for the DRB 1 *04 positive RA patients.	N/A	9098447	Details
HLA-DRB1	genotype	DRB1×04:03-DQB1×03:02	PCR	MS	Disease risk	Frequency distribution of the DRB1-DQB1 haplotypes in patients with MS and controls.	N/A	33657520	Details
IL10	allele	IL-10R2-4	PCR	MS	Disease risk	No other allele showed a significant difference between patients and controls, and the TDT analysis yielded negative results.	N/A	12101075	Details
SYN3	SNP	rs133946	PCR	MS	Disease risk	The rs133946C/C haplotype was overrepresented in the control group as compared with the MS group, but this difference did not reach statistical significance.	Synapsins are a family of four neuron-specific phosphoproteins that play a role in short-term regulation of neurotransmitter release.	18755822	Details
NOS2	SNP	rs2301369	PCR	MS	Disease risk	No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs	No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs	21376344	Details
IL23R	SNP	rs1884444	PCR	MS	Disease risk	We conclude that variants in IL-23A and IL-23R genes were associated with the risk of MS or other IDD diseases.	Interleukin-23A (IL23A) regulates and coordinates the activities of immune cells by interacting with its receptor IL23R and plays key roles in the pathogenesis of immune inflammatory diseases.	27893410	Details
IRF5	N/A	rs4728142	PCR	MS	Disease risk	Two single nucleotide polymorphism (SNPs) (rs4728142, rs3807306), and a 5 bp insertion-deletion polymorphism located in the promoter and first intron of the IRF5 gene, showed association signals with values of p,0.001 when the data from all cohorts were combined.The predisposing alleles were present on the same common haplotype in all populations. Using electrophoretic mobility shift assays we observed allele specific differences in protein binding for the SNP rs4728142 and the 5 bp indel, and by a proximity ligation assay we demonstrated increased binding of the transcription factor SP1 to the risk allele of the 5 bp indel.	IRF5 is a transcription factor involved both in the type I interferon and the toll-like receptor signalling pathways	18285424	Details
HLA-DRB1	polymorphisms	DRB1*03	PCR	MS	Phenotype risk	The other alleles did not show differences.	N/A	21418440	Details
HLA-A	allele	A19	PCR	MS	Disease risk	HLA-DR, HLA-B, and HLA-A allele frequencies in Norwegian multiple sclerosis (MS) cases and controls	N/A	14989713	Details
HLA-DPB1	polymorphism	DPB1*0501	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
LTA	polymorphisms	TNF-b*1/*1	PCR	MS	Disease risk	However, the co-occurrence of HLA-DRB 1 * 15,16 and the TNF-b*2 allele gives rise to a slightly increased relative risk for MS(RR =5.39). No such increase was found for the DRB 1 *04 positive RA patients.	N/A	9098447	Details
HLA-DRB1	genotype	DRB1×07:01-DQB1×02:01	PCR	MS	Disease risk	Frequency distribution of the DRB1-DQB1 haplotypes in patients with MS and controls.	N/A	33657520	Details
SYN3	SNP	rs133945	PCR	MS	Disease risk	The rs13945G/G haplotype was overrepresented in the control group as compared with the MS group, but this difference did not reach statistical significance.	Synapsins are a family of four neuron-specific phosphoproteins that play a role in short-term regulation of neurotransmitter release.	18755822	Details
NOS2	SNP	rs8078340	PCR	MS	Disease risk	No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs	No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs	21376344	Details
IL10	Allele	NA	PCR	MS	Disease risk	Although the size of the study group is small, these results indicate that polymorphic variations of two of the major anti-inflammatory cytokines, IL-10 and TGF-h, may play a role in MS susceptibility.	Dysregulation in the expression of pro- and anti-inflammatory cytokines is one of the milestones in multiple sclerosis (MS) development and progression. The aim of this study was to investigate the possible influence of TNF-a (?308), TGF-h (codons 10 and 25), IL-10 (?1082, ?819, ?592), IL-6 (?174) and IFN-g (+ 874) polymorphisms on susceptibility to multiple sclerosis (MS).	16183136	Details
VDR	SNP	rs10735810	PCR	MS	N/A	No association of Fok-I VDR genotype with MS	N/A	19178954	Details
IRF5	N/A	rs3807306	PCR	MS	Disease risk	Two single nucleotide polymorphism (SNPs) (rs4728142, rs3807306), and a 5 bp insertion-deletion polymorphism located in the promoter and first intron of the IRF5 gene, showed association signals with values of p,0.001 when the data from all cohorts were combined.The predisposing alleles were present on the same common haplotype in all populations. Using electrophoretic mobility shift assays we observed allele specific differences in protein binding for the SNP rs4728142 and the 5 bp indel, and by a proximity ligation assay we demonstrated increased binding of the transcription factor SP1 to the risk allele of the 5 bp indel.	IRF5 is a transcription factor involved both in the type I interferon and the toll-like receptor signalling pathways	18285424	Details
HLA-DRB1	polymorphisms	DRB1*04	PCR	MS	Phenotype risk	The other alleles did not show differences.	N/A	21418440	Details
TRB	rearrangement	N/A	PCR	MS	Disease risk	Interestingly, the DR2-restricted T cell clones displayed a biased V gene usage for Vα3 and Vα8, while Vβ gene rearrangements were highly heterogeneous.	N/A	9701037	Details
HLA-DPB1	polymorphism	DPB1*0201	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
LTA	polymorphisms	TNF-b*1/*2	PCR	MS	Disease risk	However, the co-occurrence of HLA-DRB 1 * 15,16 and the TNF-b*2 allele gives rise to a slightly increased relative risk for MS(RR =5.39). No such increase was found for the DRB 1 *04 positive RA patients.	N/A	9098447	Details
HLA-DRB1	genotype	DRB1×07:01-DQB1×03:03	PCR	MS	Disease risk	Frequency distribution of the DRB1-DQB1 haplotypes in patients with MS and controls.	N/A	33657520	Details
APOC2	allele	(TG)n(AG)m allele	PCR	MS	Disease risk	The distribution of microsatellite alleles differed between patients and controls , showing a signicant effect with MS due to the increased frequency of the allele 6 and a decrease frequency of allele 1.	APOE has a special relevance to the nervous system: evidence suggests APOE-dependent uptake of lipoproteins may play an important role in the development and maintenace of the nervous system, and in responses to both peripheral and central nervous injury.	10335523	Details
NOS2	SNP	rs9282799	PCR	MS	Disease risk	No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs	No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs	21376344	Details
TYK2	SNP	rs55762744	PCR	MS	Disease risk	Within this pedigree, rs55762744 is common and appears to be a modifier of modest risk effect.	To identify rare variants contributing to multiple sclerosis (MS) susceptibility in a family we have previously reported with up to 15 individuals affected across 4 generations.	22744673	Details
APOE	epsilon4	N/A	PCR	MS	N/A	Although the low rate of epsilon4 allele in Japan should be taken into consideration, our results showed no relation between APOE gene polymorphisms and Japanese patients with MS.	N/A	12926843	Details
HLA-DRB1	polymorphisms	DRB1*07	PCR	MS	Phenotype risk	The other alleles did not show differences.	N/A	21418440	Details
HLA-DPB1	polymorphism	DPB1*0202	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
LTA	polymorphisms	TNF-b*2/*2	PCR	MS	Disease risk	However, the co-occurrence of HLA-DRB 1 * 15,16 and the TNF-b*2 allele gives rise to a slightly increased relative risk for MS(RR =5.39). No such increase was found for the DRB 1 *04 positive RA patients.	N/A	9098447	Details
HLA-DRB1	genotype	DRB1×08:03-DQB1×03:01	PCR	MS	Disease risk	Frequency distribution of the DRB1-DQB1 haplotypes in patients with MS and controls.	N/A	33657520	Details
NOS2	SNP	rs2779248	PCR	MS	Disease risk	No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs	No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs	21376344	Details
HLA-DRB1	DRB 1" 1501	N/A	PCR	MS	Disease risk	The putative class II haplotype DRB 1" 1501-DQA 1"0102-DQB 1"0602 was found to be positively associated with MS in our Swedish patients.	N/A	8181961	Details
IL7R	N/A	rs6897932	PCR	MS	Disease risk	We found no significant difference in genotype or allele frequencies between controls and patients with multiple sclerosis either separately in Serbian, Croatian, and Slovenian populations or in the whole sample from the Western Balkans. The odds ratio for multiple sclerosis in this study was 1.04 (0.86–1.25) for the C allele	The IL7R complex is a heterodimer consisting of the IL7R alpha (IL7RA) chain and the common gamma chain (gc).3 Alternative splicing of exon 6 of IL7RA leads to the production of a membrane-bound or a soluble form of IL7RA	20194581	Details
HLA-DRB1	polymorphisms	DRB1*08	PCR	MS	Phenotype risk	The other alleles did not show differences.	N/A	21418440	Details
IL4	genotype	5V(-523) CC	PCR	MS	Disease risk	Genotype distribution and case-control analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DPB1	polymorphism	DPB1*0301	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
HLA-DRB1	polymorphisms	DRB1*1501	PCR	MS	Disease risk	Novel DR,DQ linkage disequilibrium relationship in Hong Kong Chinese have permitted recognition of DQB1*0602 as a susceptibility allele in DRZpositive MS patients, although a role for the DRBl*1501 allele in MS pathogenesis has not been excluded by this study.	N/A	1567812	Details
HLA-DRB1	genotype	DRB1×10:01-DQB1×05:01	PCR	MS	Disease risk	Frequency distribution of the DRB1-DQB1 haplotypes in patients with MS and controls.	N/A	33657520	Details
NOS2	SNP	rs3730013	PCR	MS	Disease risk	No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs	No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs	21376344	Details
HLA-DRB1	polymorphisms	DRB1*09	PCR	MS	Phenotype risk	The other alleles did not show differences.	N/A	21418440	Details
IL4	genotype	5V(-523) CT	PCR	MS	Disease risk	Genotype distribution and case-control analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DPB1	polymorphism	DPB1*0401	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
HLA-DRB1	polymorphisms	DRB1*1502	PCR	MS	Disease risk	Novel DR,DQ linkage disequilibrium relationship in Hong Kong Chinese have permitted recognition of DQB1*0602 as a susceptibility allele in DRZpositive MS patients, although a role for the DRBl*1501 allele in MS pathogenesis has not been excluded by this study.	N/A	1567812	Details
HLA-DRB1	genotype	DRB1×11:01-DQB1×03:01	PCR	MS	Disease risk	Frequency distribution of the DRB1-DQB1 haplotypes in patients with MS and controls.	N/A	33657520	Details
NOS2	SNP	rs3794764	PCR	MS	Disease risk	No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs	No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs	21376344	Details
CIITA	Allele	NA	PCR	MS	Disease risk	Carriage of 11614C was protective against JIA (OR 0.6, 95% CI 0.3–1.0) and showed a similar trend in RA and MS (OR 0.7, 95% CI 0.5–1.0; OR 0.8, 95% CI 0.6–1.0, respectively).	The 2168A-G polymorphism has been shown to influence transcription of the MHC2TA gene and has been implicated in several inflammatory/autoimmune disorders.	29100048	Details
HLA-DRB1	polymorphisms	DRB1*10	PCR	MS	Phenotype risk	The other alleles did not show differences.	N/A	21418440	Details
IL4	genotype	5V(-523) TT	PCR	MS	Disease risk	Genotype distribution and case-control analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DPB1	polymorphism	DPB1*0402	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
HLA-DRB1	polymorphisms	DRB1*1602	PCR	MS	Disease risk	Novel DR,DQ linkage disequilibrium relationship in Hong Kong Chinese have permitted recognition of DQB1*0602 as a susceptibility allele in DRZpositive MS patients, although a role for the DRBl*1501 allele in MS pathogenesis has not been excluded by this study.	N/A	1567812	Details
HLA-DRB1	genotype	DRB1×13:02-DQB1×06:01	PCR	MS	Disease risk	Frequency distribution of the DRB1-DQB1 haplotypes in patients with MS and controls.	N/A	33657520	Details
NOS2	SNP	rs3729508	PCR	MS	Disease risk	No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs	No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs	21376344	Details
PRF1	SNP	rs885822	PCR	MS	Phenotypic risk	We genotyped three PRF1 single nucleotide polymorphisms (rs885822, rs10999426, and rs3758562) in 420 patients with MS and 512 controls.	The granule-dependent exocytosis pathway is an important mechanism to induce apoptosis by CD8+ T cells and NK cells and involves lytic molecules such as perforin.	20921521	Details
HLA-DRB1	polymorphisms	DRB1*11	PCR	MS	Phenotype risk	The other alleles did not show differences.	N/A	21418440	Details
IL4	allele	5V(-523) C	PCR	MS	Disease risk	Genotype distribution and case-control analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DPB1	polymorphism	DPB1*0501	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
HLA-DRB5	polymorphisms	DRB5*0101	PCR	MS	Disease risk	Novel DR,DQ linkage disequilibrium relationship in Hong Kong Chinese have permitted recognition of DQB1*0602 as a susceptibility allele in DRZpositive MS patients, although a role for the DRBl*1501 allele in MS pathogenesis has not been excluded by this study.	N/A	1567812	Details
HLA-DRB1	genotype	DRB1×13:01-DQB1×06:01	PCR	MS	Disease risk	Frequency distribution of the DRB1-DQB1 haplotypes in patients with MS and controls.	N/A	33657520	Details
NOS2	SNP	rs1137933	PCR	MS	Disease risk	No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs	No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs	21376344	Details
PRF1	SNP	rs10999426	PCR	MS	Phenotypic risk	We genotyped three PRF1 single nucleotide polymorphisms (rs885822, rs10999426, and rs3758562) in 420 patients with MS and 512 controls.	The granule-dependent exocytosis pathway is an important mechanism to induce apoptosis by CD8+ T cells and NK cells and involves lytic molecules such as perforin.	20921521	Details
IL12B	SNP	rs17860508	PCR	MS	Disease risk	Our results suggest that sex-specific effects of IL12B polymorphisms, rs17860508 and rs3212227, on genetic predisposition and disease course of RRMS, is probably mediated by their gender-dependent functional effect on IL-12p40-containing cytokines.	Our results suggest that sex-specific effects of IL12B polymorphisms, rs17860508 and rs3212227, on genetic predisposition and disease course of RRMS, is probably mediated by their gender-dependent functional effect on IL-12p40-containing cytokines.	30554348	Details
HLA-DRB1	polymorphisms	DRB1*12	PCR	MS	Phenotype risk	The other alleles did not show differences.	N/A	21418440	Details
IL4	allele	5V(-523) T	PCR	MS	Disease risk	Genotype distribution and case-control analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DPB1	polymorphism	DPB1*0601	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
HLA-DRB5	polymorphisms	DRB5*0102	PCR	MS	Disease risk	Novel DR,DQ linkage disequilibrium relationship in Hong Kong Chinese have permitted recognition of DQB1*0602 as a susceptibility allele in DRZpositive MS patients, although a role for the DRBl*1501 allele in MS pathogenesis has not been excluded by this study.	N/A	1567812	Details
HLA-DRB1	genotype	DRB1×14:04-DQB1×05:03	PCR	MS	Disease risk	Frequency distribution of the DRB1-DQB1 haplotypes in patients with MS and controls.	N/A	33657520	Details
HLA-DRB1	allele	N/A	PCR	MS	Disease risk	No significant increase in the frequency of DR2 alleles was detected among MS patients.	N/A	7605774	Details
NOS2	SNP	rs4796052	PCR	MS	Disease risk	No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs	No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs	21376344	Details
PRF1	SNP	rs3758562	PCR	MS	Phenotypic risk	We genotyped three PRF1 single nucleotide polymorphisms (rs885822, rs10999426, and rs3758562) in 420 patients with MS and 512 controls.	The granule-dependent exocytosis pathway is an important mechanism to induce apoptosis by CD8+ T cells and NK cells and involves lytic molecules such as perforin.	20921521	Details
IL12B	SNP	rs3212227	PCR	MS	Disease risk	Our results suggest that sex-specific effects of IL12B polymorphisms, rs17860508 and rs3212227, on genetic predisposition and disease course of RRMS, is probably mediated by their gender-dependent functional effect on IL-12p40-containing cytokines.	Our results suggest that sex-specific effects of IL12B polymorphisms, rs17860508 and rs3212227, on genetic predisposition and disease course of RRMS, is probably mediated by their gender-dependent functional effect on IL-12p40-containing cytokines.	30554348	Details
HLA-DRB1	polymorphisms	DRB1*13	PCR	MS	Phenotype risk	The other alleles did not show differences.	N/A	21418440	Details
IL4	genotype	E1(33) CC	PCR	MS	Disease risk	Genotype distribution and case-control analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DPB1	polymorphism	DPB1*0901	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
HLA-DRB5	polymorphisms	DRB5*new	PCR	MS	Disease risk	Novel DR,DQ linkage disequilibrium relationship in Hong Kong Chinese have permitted recognition of DQB1*0602 as a susceptibility allele in DRZpositive MS patients, although a role for the DRBl*1501 allele in MS pathogenesis has not been excluded by this study.	N/A	1567812	Details
HLA-DRB1	genotype	DRB1×15:01 a-DQB1×05:01	PCR	MS	Disease risk	Frequency distribution of the DRB1-DQB1 haplotypes in patients with MS and controls.	N/A	33657520	Details
SLC6A4	polymorphisms	5-HTTLPR, rs35521, and STin2VNTR	PCR	MS	Disease risk	The frequencies of alleles, genotypes, genotype combinations, and haplotypes did not differ significantly between patients with MS and healthy controls.	Serotonin (5-hydroxytryptamine) plays a pivotal role in the pathophysiology of most neuropsychiatric disorders.Serotonin level itself is controlled by serotonin reuptake transporter (SERT) gene on chromosome 17q11.2, and different polymorphisms affect the transcription activity of this gene, leading to impaired serotonin reuptake.	30886676	Details
HLA-DQB1	allele	N/A	PCR	MS	Disease risk	No significant association was found with the glutamine residue at position 34 of the DQ alpha chain.	N/A	7605774	Details
NOS2	SNP	rs2248814	PCR	MS	Disease risk	No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs	No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs	21376344	Details
GALR2	SNP	rs61745847	PCR	MS	up-regulation	Here, after performing whole exome sequencing, we found a MS patient harboring a rare and homozygous single nucleotide variant (SNV; rs61745847) of the G-protein coupled receptor (GPCR) galanin-receptor 2 (GALR2) that alters an important amino acid in the TM6 molecular toggle switch region (W249L).	Even though the etiology of MS remains unknown, it is accepted that it involves a combination of genetic alterations and environmental factors.	30131588	Details
HLA-DRB1	polymorphisms	DRB1*14	PCR	MS	Phenotype risk	The other alleles did not show differences.	N/A	21418440	Details
IL4	genotype	E1(33) TT	PCR	MS	Disease risk	Genotype distribution and case-control analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DPB1	polymorphism	DPB1*1301	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
HLA-DQA1	polymorphisms	DQA1*0101	PCR	MS	Disease risk	Novel DR,DQ linkage disequilibrium relationship in Hong Kong Chinese have permitted recognition of DQB1*0602 as a susceptibility allele in DRZpositive MS patients, although a role for the DRBl*1501 allele in MS pathogenesis has not been excluded by this study.	N/A	1567812	Details
HLA-DRB1	genotype	DRB1×15:01a-DQB1×06:02	PCR	MS	Disease risk	Univariate analysis of IL7R SNP (rs6897932) showed no significant association with MS in our population whereas analysis of HLA-DRB1 alleles and IL7R (rs6897932) genotypes showed significant association between the HLA-DRB1*15:01/15:02 and the IL7R (rs6897932) CC genotype (OR = 3.58, p = 0.0002).	N/A	33657520	Details
NOS2	SNP	rs2297518	PCR	MS	Disease risk	No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs	No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs	21376344	Details
LEP	Allele	NA	PCR	MS	Disease risk	Our study implicates a significant role of LEP and LEPR polymorphisms and also leptin levels in the risk of MS and its severity.	Leptin, the product of the ob gene, can modulate the immune responses and also seems to regulate Th1/Th2 balance by promoting a shift from the Th2 to the Th1 inflammatory cytokine pathway.	27105071	Details
HLA-DRB1	polymorphisms	DRB1*15	PCR	MS	Phenotype risk	HLA-DRB1*15 allele is associated with OCB-positive patients with MS when studying a Spanish MS population	This hypothesis may be supported by previous published results in which DRB1*1501 patients showed elevated levels of inflammation in CSF, such as higher IgG synthesis levels, matrix metalloproteinase-9 activity, and an altered T-cell activation status.	21418440	Details
IL4	genotype	E1(33) CT	PCR	MS	Disease risk	Genotype distribution and case-control analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DPB1	polymorphism	DPB1*1401	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
HLA-DQA1	polymorphisms	DQA1*0102	PCR	MS	Disease risk	Novel DR,DQ linkage disequilibrium relationship in Hong Kong Chinese have permitted recognition of DQB1*0602 as a susceptibility allele in DRZpositive MS patients, although a role for the DRBl*1501 allele in MS pathogenesis has not been excluded by this study.	N/A	1567812	Details
IL7R	SNP	rs6897932(CC)	PCR	MS	Disease risk	Univariate analysis of IL7R SNP (rs6897932) showed no significant association with MS in our population whereas analysis of HLA-DRB1 alleles and IL7R (rs6897932) genotypes showed significant association between the HLA-DRB1*15:01/15:02 and the IL7R (rs6897932) CC genotype (OR = 3.58, p = 0.0002).	N/A	33657520	Details
NOS2	SNP	rs1060826	PCR	MS	Disease risk	No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs	No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs	21376344	Details
LEPR	Allele	NA	PCR	MS	Disease risk	Our study implicates a significant role of LEP and LEPR polymorphisms and also leptin levels in the risk of MS and its severity.	Leptin, the product of the ob gene, can modulate the immune responses and also seems to regulate Th1/Th2 balance by promoting a shift from the Th2 to the Th1 inflammatory cytokine pathway.	27105071	Details
PDCD1	SNP	rs11568821	PCR	MS	Disease risk	Our population-based case-control study, investigating selected three PD-1 SNPs: PD-1.3, PD-1.5 and PD-1.9, revealed that polymorphic variation may be rather disease-modifying than MS risk factor.	N/A	28284331	Details
HLA-DRB1	polymorphisms	DRB1*16	PCR	MS	Phenotype risk	The other alleles did not show differences.	N/A	21418440	Details
IL4	allele	E1(33) C	PCR	MS	Disease risk	Genotype distribution and case-control analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DPB1	polymorphism	DPB1*1701	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
HLA-DQA1	polymorphisms	DQA1*0103	PCR	MS	Disease risk	Novel DR,DQ linkage disequilibrium relationship in Hong Kong Chinese have permitted recognition of DQB1*0602 as a susceptibility allele in DRZpositive MS patients, although a role for the DRBl*1501 allele in MS pathogenesis has not been excluded by this study.	N/A	1567812	Details
MBP	polymorphism	N/A	PCR	MS	Disease risk ,Phenotypic risk	The results of ourstudy indicate a signicantly different distributionof the hMBP polymorphism pattern in relapsing remitting MS patients compared to healthy controls.More specically, the short 354 bp hMBP frag-ment was more frequent in relapsing remitting MS patients than in primary chronic progressive MS and controls,whereas the long 424 bp hMBP fragment was more frequent than the short one inthe whole population studied and particularly inthe healthy controls.	Human myelin basic protein (hMBP) could act as anautoantigen and thus intervene in the pathogenicmechanism of multiple sclerosis (MS), moreover thehMBP gene has been suggested as one of the genesinvolved in MS susceptibility.	10871781	Details
NOS2	SNP	rs8081248	PCR	MS	Disease risk	No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs	No significant association between cases and controls (P>0.05) was observed for the alleles of the SNPs	21376344	Details
IL6	SNP	rs1800795	PCR	MS	Disease risk	We also showed that IL-12B A1188C (rs3212227) can contribute to the progression of the disease in the Czech population.	Pro-inflammatory and anti-inflammatory cytokines have been shown to play a crucial role in the pathophysiology of multiple sclerosis (MS)	30069682	Details
PDCD1	SNP	rs2227981	PCR	MS	Disease risk	Our population-based case-control study, investigating selected three PD-1 SNPs: PD-1.3, PD-1.5 and PD-1.9, revealed that polymorphic variation may be rather disease-modifying than MS risk factor.	N/A	28284331	Details
TRB	expansion	Vβ1	PCR	MS	Disease risk	The frequency of Vβ expansion in healthy subjects and patients with MS during active and remission phasesa	immunotherapy with TCR DNA vaccines targeting Vβs selected by spectratyping analysis successfully suppressed the development of autoimmune diseases.	12707368	Details
IL4	allele	E1(33) T	PCR	MS	Disease risk	Genotype distribution and case-control analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DPB1	polymorphism	DPB1*1901	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
HLA-DQB1	polymorphisms	DQB1*0501	PCR	MS	Disease risk	Novel DR,DQ linkage disequilibrium relationship in Hong Kong Chinese have permitted recognition of DQB1*0602 as a susceptibility allele in DRZpositive MS patients, although a role for the DRBl*1501 allele in MS pathogenesis has not been excluded by this study.	N/A	1567812	Details
ITGA4	SNP	Rs155141	PCR	MS	Disease risk	Although this study has failed to find any associations, we suggest that further studies should fully assess the contribution of this gene to MS susceptibility.	N/A	17689671	Details
MMP9	polymorphisms	1562 C/T	PCR	MS	Disease risk	A significant upper difference was observed in allele frequencies between MS patients compared to healthy volunteers in 1562C/T MMP-9 gene polymorphism. Additionally, frequency distribution of MMP-9 genotypes has a significant relationship with MS disease;in such a way that CC+CT genotype opposed to TT showed a significant association with MS.	The episodic phase of relapsing-remitting (RR) MS is characterized by the breakdown of the blood-brain barrier (BBB), autoreactive inflammatory cells migrating into the CNS and demyelination.Matrix metalloproteinases (MMPs) are proteolytic enzymes implicated in many aspects of human development and tissue remodeling.These enzymes, particularly Matrix metalloproteinase-9 (MMP-9), are the major participants in breakdown of the blood-brain barrier (BBB) in MS. MMP-9, also known as gelatinase B, degrades various components of the extracellular matrix (ECM).MMP9 plays a role in the inflammatory cells influx in the CNS and have been revealed to split human myelin basic protein (MBP).The single nucleotide polymorphism C–1562 T prevents the binding of a nuclear repressor protein to this region of the MMP-9 gene promoter, then attending to raised MMP-9 expression, as reported in vitro studies.	31700826	Details
IL1RN	allele	A2+,A2-	PCR	MS	Disease risk	Among MS patients, there was a significantly increased frequency of IL-1RA allele 2 carriers in women as compared to men. IL-1RA allele 2 carriers were more frequently women with MS than control women.No significant associations were found in two-locus combinations of the allele 2 carriers and non-carriers.	Interleukin-1β( IL-1β) is a strong proinflammatory cytokine produced abundantly in acute and chronic active lesions of multiple sclerosis MS. The activity of IL-1 can be inhibited by IL-1 receptor antagonist IL-1RA ,which binds the IL-1 receptor but does not transmit the agonist signal.	11311293	Details
IL-12	SNP	rs3212227	PCR	MS	Disease risk	We also showed that IL-12B A1188C (rs3212227) can contribute to the progression of the disease in the Czech population.	Pro-inflammatory and anti-inflammatory cytokines have been shown to play a crucial role in the pathophysiology of multiple sclerosis (MS)	30069682	Details
PDCD1	SNP	rs2227982	PCR	MS	Disease risk	Our population-based case-control study, investigating selected three PD-1 SNPs: PD-1.3, PD-1.5 and PD-1.9, revealed that polymorphic variation may be rather disease-modifying than MS risk factor.	N/A	28284331	Details
TRB	expansion	Vβ2	PCR	MS	Disease risk	The frequency of Vβ expansion in healthy subjects and patients with MS during active and remission phasesa	immunotherapy with TCR DNA vaccines targeting Vβs selected by spectratyping analysis successfully suppressed the development of autoimmune diseases.	12707368	Details
IL4	genotype	I3(709)	PCR	MS	Disease risk	I3(709)*VNTR was associated with susceptibility to MS ( p = 0.004) due to a dearth of heterozygotes in patients (29/122; 23.8%) compared to controls (91/244; 37.3%).	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DRB1	polymorphism	DRB1*0101	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
HLA-DQB1	polymorphisms	DQB1*0502	PCR	MS	Disease risk	Novel DR,DQ linkage disequilibrium relationship in Hong Kong Chinese have permitted recognition of DQB1*0602 as a susceptibility allele in DRZpositive MS patients, although a role for the DRBl*1501 allele in MS pathogenesis has not been excluded by this study.	N/A	1567812	Details
ITGA4	SNP	Rs1449263	PCR	MS	Disease risk	Carriage of the C allele of the ITGA4 promoter SNP rs1449263 was independently and weakly increased in MS patients from each population compared to respective controls (P= 0.037 in Basque; and P= 0.042 in Nordic cohorts), though these associations were lost upon application of permutation correction.	N/A	17689671	Details
PNMT	polymorphism	G (-387)/A (-387) and G (-182)/A (-182)	PCR	MS	Disease risk	In subjects with MS, significant differences in the frequency of the GG genotype at the G-387A marker and the AA genotype at the G-182A marker were observed. Additionally, when both markers were combined and evaluated, highly significant differences between the polymorphism distributions in patients with MS and control subjects were detected. The data suggest that these promoter polymorphisms of the PNMT gene, both independently and cumulatively, show association with MS.	PNMT is a specific marker for adrenergic neurons and nerve fibers because it mediates the conversion of norepinephrine (NE) to epinephrine (EPI), suggesting that PNMT is an important enzyme in the metabolism of both of these neurotransmitters. In MS, the immune system mistakenly attacks self-molecules found within the brain and spinal cord. Cytokines are thought to play an intimate role in the progression of these biological effects on the CNS.	11958827	Details
TRB	expansion	Vβ3	PCR	MS	Disease risk	The frequency of Vβ expansion in healthy subjects and patients with MS during active and remission phasesa	immunotherapy with TCR DNA vaccines targeting Vβs selected by spectratyping analysis successfully suppressed the development of autoimmune diseases.	12707368	Details
IL4	genotype	I3(709) 11	PCR	MS	Disease risk	Genotype distribution and case-control analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DRB1	polymorphism	DRB1*1501	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
HLA-DQB1	polymorphisms	DQB1*0601	PCR	MS	Disease risk	Novel DR,DQ linkage disequilibrium relationship in Hong Kong Chinese have permitted recognition of DQB1*0602 as a susceptibility allele in DRZpositive MS patients, although a role for the DRBl*1501 allele in MS pathogenesis has not been excluded by this study.	N/A	1567812	Details
ITGA4	SNP	Rs3770138	PCR	MS	Disease risk	Although this study has failed to find any associations, we suggest that further studies should fully assess the contribution of this gene to MS susceptibility.	N/A	17689671	Details
IL17F	SNP	rs763780	PCR	MS	Disease risk	A significantly increased frequency of rs763780 TT genotype	These results suggest that rs763780 is associated with multiple sclerosis in a Chinese Han population.	24857622	Details
HLA-DRB1	Allele	NA	PCR	MS	Phenotypic risk	Our study suggests that MS patients harboring DRB1*0405, a genetic risk factor for MS in the Japanese population, have a younger age at onset and a relatively benign disease course, while DRB1*0405-negative MS patients have features similar to Western-type MS in terms of association with Epstein-Barr virus infection and DRB1*1501. The recent increase of MS in young Japanese people may be caused, in part, by an increase in DRB1*0405-positive MS patients.	Nationwide surveys conducted in Japan over the past thirty years have revealed a four-fold increase in the estimated number of multiple sclerosis (MS) patients, a decrease in the age at onset, and successive increases in patients with conventional MS, which shows an involvement of multiple sites in the central nervous system, including the cerebrum and cerebellum. We aimed to clarify whether genetic and infectious backgrounds correlate to distinct disease phenotypes of MS in Japanese patients.	23152786	Details
TRB	expansion	Vβ4	PCR	MS	Disease risk	The frequency of Vβ expansion in healthy subjects and patients with MS during active and remission phasesa	immunotherapy with TCR DNA vaccines targeting Vβs selected by spectratyping analysis successfully suppressed the development of autoimmune diseases.	12707368	Details
IL4	genotype	I3(709) 12	PCR	MS	Disease risk	Genotype distribution and case-control analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DRB1	polymorphism	DRB1*1502	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
HLA-DQB1	polymorphisms	DQB1*0602	PCR	MS	Disease risk	Novel DR,DQ linkage disequilibrium relationship in Hong Kong Chinese have permitted recognition of DQB1*0602 as a susceptibility allele in DRZpositive MS patients, although a role for the DRBl*1501 allele in MS pathogenesis has not been excluded by this study.	N/A	1567812	Details
ITGA4	SNP	Rs3770136	PCR	MS	Disease risk	Although this study has failed to find any associations, we suggest that further studies should fully assess the contribution of this gene to MS susceptibility.	N/A	17689671	Details
IL17A	SNP	rs2275913	PCR	MS	Disease risk	The genotypic and allelic frequencies of rs2275913 in IL-17A gene were not different between patients with MS and controls	N/A	24857622	Details
TRB	expansion	Vβ5.1	PCR	MS	Disease risk	The frequency of Vβ expansion in healthy subjects and patients with MS during active and remission phasesa	immunotherapy with TCR DNA vaccines targeting Vβs selected by spectratyping analysis successfully suppressed the development of autoimmune diseases.	12707368	Details
IL4	genotype	I3(709) 22	PCR	MS	Disease risk	Genotype distribution and case-control analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DRB1	polymorphism	DRB1*1602	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
HLA-DQB1	polymorphisms	DQB1*0603	PCR	MS	Disease risk	Novel DR,DQ linkage disequilibrium relationship in Hong Kong Chinese have permitted recognition of DQB1*0602 as a susceptibility allele in DRZpositive MS patients, although a role for the DRBl*1501 allele in MS pathogenesis has not been excluded by this study.	N/A	1567812	Details
ITGA4	SNP	Rs3770132	PCR	MS	Disease risk	Although this study has failed to find any associations, we suggest that further studies should fully assess the contribution of this gene to MS susceptibility.	N/A	17689671	Details
SPARCL1	SNP	rs1049539	PCR	MS	N/A	One hundred eighty-six patients with MS and 185 age-matched controls were genotyped for A/G single nucleotide polymorphism (SNP) in exon 1 (rs1049539), C/G SNP in exon 4 (rs1049544), resulting in a substitution of an aspartate with an histidine, and A/G substitution in the exon 5 (rs1130643), leading to the substitution of alanine with threonine. No significant differences in either allelic or genotypic frequency of the three SNPs were found (P>0.05), even in stratifying MS patients according to the course of the disease.	N/A	17825989	Details
IL7R	SNP	rs6897932	PCR	MS	Disease risk	In total, 197 Indian patients and 197 unrelated controls were analyzed. The most associated single nucleotide polymorphism (SNP) within this study was rs6897932 in the IL7R gene, which showed a strong protective effect in this data set (rs 6897932, OR 0.5543, 95% CI 0.37–0.78, p 0.0009727). Two other SNPs were nominally associated with MS in this dataset, namely CLEC16A rs 12708716 (p 0.0082, OR 1.478, 95% CI 1.106–1.975) and CD226 rs763361 (p 0.03971, OR 1.353, CI 1.014–1.805). For the majority of the remaining SNPs (7/14), the trend for association was in the same direction as in previous studies in the white population	in Asian and Western MS. Analysis of the HLA class II genes, DRB1, DQA1 and DQB1 in a limited number of cases revealed the expected association with the European susceptibility haplotype DRB1*1501–DQB1*0602	20952449	Details
TRB	expansion	Vβ5.2	PCR	MS	Disease risk	These findings suggest that Vβ5.2 spectratype expansion is associated with the development of MS.	immunotherapy with TCR DNA vaccines targeting Vβs selected by spectratyping analysis successfully suppressed the development of autoimmune diseases.	12707368	Details
IL4	allele	I3(709) 1	PCR	MS	Disease risk	Genotype distribution and case-control analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DRB1	polymorphism	DRB1*0303	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
ITGA4	SNP	Rs155106	PCR	MS	Disease risk	Although this study has failed to find any associations, we suggest that further studies should fully assess the contribution of this gene to MS susceptibility.	N/A	17689671	Details
Zhx2	allele	N/A	PCR	EAE	Disease risk	Mutant Afr-1 allele expressed by BALB/cJ mice did not segregate with disease resistance.EAE resistance is currently unassociated with any other known phenotypic differences characterizing BALB/cJ mice.	N/A	2458211	Details
SPARCL1	SNP	rs1049544	PCR	MS	N/A	One hundred eighty-six patients with MS and 185 age-matched controls were genotyped for A/G single nucleotide polymorphism (SNP) in exon 1 (rs1049539), C/G SNP in exon 4 (rs1049544), resulting in a substitution of an aspartate with an histidine, and A/G substitution in the exon 5 (rs1130643), leading to the substitution of alanine with threonine. No significant differences in either allelic or genotypic frequency of the three SNPs were found (P>0.05), even in stratifying MS patients according to the course of the disease.	N/A	17825989	Details
CLEC16A	SNP	rs 12708716	PCR	MS	Disease risk	In total, 197 Indian patients and 197 unrelated controls were analyzed. The most associated single nucleotide polymorphism (SNP) within this study was rs6897932 in the IL7R gene, which showed a strong protective effect in this data set (rs 6897932, OR 0.5543, 95% CI 0.37–0.78, p 0.0009727). Two other SNPs were nominally associated with MS in this dataset, namely CLEC16A rs 12708716 (p 0.0082, OR 1.478, 95% CI 1.106–1.975) and CD226 rs763361 (p 0.03971, OR 1.353, CI 1.014–1.805). For the majority of the remaining SNPs (7/14), the trend for association was in the same direction as in previous studies in the white population	in Asian and Western MS. Analysis of the HLA class II genes, DRB1, DQA1 and DQB1 in a limited number of cases revealed the expected association with the European susceptibility haplotype DRB1*1501–DQB1*0602	20952449	Details
TRB	expansion	Vβ6	PCR	MS	Disease risk	The frequency of Vβ expansion in healthy subjects and patients with MS during active and remission phasesa	immunotherapy with TCR DNA vaccines targeting Vβs selected by spectratyping analysis successfully suppressed the development of autoimmune diseases.	12707368	Details
IL4	allele	I3(709) 2	PCR	MS	Disease risk	Genotype distribution and case-control analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DRB1	polymorphism	DRB1*0401	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
ITGA4	SNP	Rs1038034	PCR	MS	Disease risk	Although this study has failed to find any associations, we suggest that further studies should fully assess the contribution of this gene to MS susceptibility.	N/A	17689671	Details
VDR	Gene polymorphisms	ApaI	PCR	MS	Disease risk	our data suggest that VDR gene polymorphisms ApaI, BsmI and TaqI are not useful in the prediction of disease disability progression rate in MS in Slovaks	Vitamin D acts through vitamin D receptor (VDR) and has promising beneficial effects in the development and progression of multiple sclerosis	27338176	Details
MMP9	Allele	NA	PCR	MS	Disease risk	No associations were found between the 17 polymorphisms and MS. Also, gene expression levels were analysed according to genotype: no associations were observed.	Matrix metalloproteinase 9 (MMP9) is involved in multiple sclerosis (MS) aetiology. Previously, we identified differen-tial gene expression of plasminogen activation cascade genes in MS patients.	23897640	Details
SPARCL1	SNP	rs1130643	PCR	MS	N/A	One hundred eighty-six patients with MS and 185 age-matched controls were genotyped for A/G single nucleotide polymorphism (SNP) in exon 1 (rs1049539), C/G SNP in exon 4 (rs1049544), resulting in a substitution of an aspartate with an histidine, and A/G substitution in the exon 5 (rs1130643), leading to the substitution of alanine with threonine. No significant differences in either allelic or genotypic frequency of the three SNPs were found (P>0.05), even in stratifying MS patients according to the course of the disease.	N/A	17825989	Details
CD226	SNP	rs763361	PCR	MS	Disease risk	In total, 197 Indian patients and 197 unrelated controls were analyzed. The most associated single nucleotide polymorphism (SNP) within this study was rs6897932 in the IL7R gene, which showed a strong protective effect in this data set (rs 6897932, OR 0.5543, 95% CI 0.37–0.78, p 0.0009727). Two other SNPs were nominally associated with MS in this dataset, namely CLEC16A rs 12708716 (p 0.0082, OR 1.478, 95% CI 1.106–1.975) and CD226 rs763361 (p 0.03971, OR 1.353, CI 1.014–1.805). For the majority of the remaining SNPs (7/14), the trend for association was in the same direction as in previous studies in the white population	in Asian and Western MS. Analysis of the HLA class II genes, DRB1, DQA1 and DQB1 in a limited number of cases revealed the expected association with the European susceptibility haplotype DRB1*1501–DQB1*0602	20952449	Details
TRB	expansion	Vβ7	PCR	MS	Disease risk	The frequency of Vβ expansion in healthy subjects and patients with MS during active and remission phasesa	immunotherapy with TCR DNA vaccines targeting Vβs selected by spectratyping analysis successfully suppressed the development of autoimmune diseases.	12707368	Details
IL4	genotype	I3(2580) CC	PCR	MS	Disease risk	Genotype distribution and case-control analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DRB1	polymorphism	DRB1*0405	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
ITGA4	SNP	Rs2305586	PCR	MS	Disease risk	Although this study has failed to find any associations, we suggest that further studies should fully assess the contribution of this gene to MS susceptibility.	N/A	17689671	Details
VDR	Gene polymorphisms	BsmI	PCR	MS	Disease risk	our data suggest that VDR gene polymorphisms ApaI, BsmI and TaqI are not useful in the prediction of disease disability progression rate in MS in Slovaks	Vitamin D acts through vitamin D receptor (VDR) and has promising beneficial effects in the development and progression of multiple sclerosis	27338176	Details
PLAU	Allele	NA	PCR	MS	Disease risk	No associations were found between the 17 polymorphisms and MS. Also, gene expression levels were analysed according to genotype: no associations were observed.	Matrix metalloproteinase 9 (MMP9) is involved in multiple sclerosis (MS) aetiology. Previously, we identified differen-tial gene expression of plasminogen activation cascade genes in MS patients.	23897640	Details
CIITA	SNP	rs4774C	PCR	MS	Disease risk	a statistical significance was found for the two polymorphisms of MHC2TA when we compared MS patients with active replication and controls (p= 0.0000004 for rs4774C and p= 0.011 for rs3087456G)	To study these questions we analyzed in a MS cohort: two polymorphisms of MHC2TA, a gene that has been previously associated with MS, and also with HHV-6, two polymorphisms of CD46, the gene that codes for the cellular receptor of HHV-6, and the HHV-6 replicative status through the analysis of HHV-6 genomes in serum samples by quantitative real-time PCR along two-year follow-up	21962857	Details
TRB	expansion	Vβ8	PCR	MS	Disease risk	The frequency of Vβ expansion in healthy subjects and patients with MS during active and remission phasesa	immunotherapy with TCR DNA vaccines targeting Vβs selected by spectratyping analysis successfully suppressed the development of autoimmune diseases.	12707368	Details
IL4	genotype	I3(2580) CA	PCR	MS	Disease risk	Genotype distribution and case-control analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DRB1	polymorphism	DRB1*0407	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
ITGA4	SNP	Rs3770115	PCR	MS	Disease risk	Although this study has failed to find any associations, we suggest that further studies should fully assess the contribution of this gene to MS susceptibility.	N/A	17689671	Details
VDR	Gene polymorphisms	TaqI	PCR	MS	Disease risk	our data suggest that VDR gene polymorphisms ApaI, BsmI and TaqI are not useful in the prediction of disease disability progression rate in MS in Slovaks	Vitamin D acts through vitamin D receptor (VDR) and has promising beneficial effects in the development and progression of multiple sclerosis	27338176	Details
SERPINB2	Allele	NA	PCR	MS	Disease risk	No associations were found between the 17 polymorphisms and MS. Also, gene expression levels were analysed according to genotype: no associations were observed.	Matrix metalloproteinase 9 (MMP9) is involved in multiple sclerosis (MS) aetiology. Previously, we identified differen-tial gene expression of plasminogen activation cascade genes in MS patients.	23897640	Details
CIITA	SNP	rs3087456G	PCR	MS	Disease risk	a statistical significance was found for the two polymorphisms of MHC2TA when we compared MS patients with active replication and controls (p= 0.0000004 for rs4774C and p= 0.011 for rs3087456G)	To study these questions we analyzed in a MS cohort: two polymorphisms of MHC2TA, a gene that has been previously associated with MS, and also with HHV-6, two polymorphisms of CD46, the gene that codes for the cellular receptor of HHV-6, and the HHV-6 replicative status through the analysis of HHV-6 genomes in serum samples by quantitative real-time PCR along two-year follow-up	21962857	Details
TRB	expansion	Vβ9	PCR	MS	Disease risk	The frequency of Vβ expansion in healthy subjects and patients with MS during active and remission phasesa	immunotherapy with TCR DNA vaccines targeting Vβs selected by spectratyping analysis successfully suppressed the development of autoimmune diseases.	12707368	Details
IL4	genotype	I3(2580) AA	PCR	MS	Disease risk	Genotype distribution and case-control analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DRB1	polymorphism	DRB1*0410	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
ITGA4	SNP	Rs3816521	PCR	MS	Disease risk	Although this study has failed to find any associations, we suggest that further studies should fully assess the contribution of this gene to MS susceptibility.	N/A	17689671	Details
STAT3	SNP	rs3809758/rs744166/rs1026916/rs12948909	PCR	MS	Disease risk	No significant differences were observed between MS patients and controls for any of the studied polymorphisms.	N/A	20200543	Details
VDR	Gene polymorphisms	BsmI BB（AA）	PCR	MS	Disease risk	We showed for the first time that BsmI genotype BB (AA) is associated with the decreased susceptibility to MS in Slovak population	Vitamin D acts through vitamin D receptor (VDR) and has promising beneficial effects in the development and progression of multiple sclerosis	27338176	Details
IL7	Allele	NA	PCR	MS	Disease risk	We found reduced IL-7Ra expression on conventional T cells and upregulated IL-7 plasma levels together with reduction of RTE-Treg frequencies and Treg function in MS, without clear genetic influence. Decreased IL-7Ra expression in MS correlated with declined dual-receptor-Treg and reduced MDC TSLPR expression, indicating contracted thymic Treg output	RTE-Treg and long-lived memory Treg coincides with the MS-associated Treg defect, as shown previously. Recent studies demonstrate that IL-7 and thymic stromal lymphopoietin (TSLP) are critical for Treg matura-tion.	21287555	Details
TRB	expansion	Vβ10	PCR	MS	Disease risk	The frequency of Vβ expansion in healthy subjects and patients with MS during active and remission phasesa	immunotherapy with TCR DNA vaccines targeting Vβs selected by spectratyping analysis successfully suppressed the development of autoimmune diseases.	12707368	Details
IL4	allele	I3(2580) A	PCR	MS	Disease risk	Genotype distribution and case-control analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DRB1	polymorphism	DRB1*1101	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
ITGA4	SNP	Rs3770111	PCR	MS	Disease risk	Although this study has failed to find any associations, we suggest that further studies should fully assess the contribution of this gene to MS susceptibility.	N/A	17689671	Details
IL2RA	SNP	rs2104286	PCR	MS	Disease risk	There were no significant differences.	IL2RA genes are involved in T cell regulation which plays an important role in the pathogenesis of autoimmune diseases besides MS.Han Chinese MS and patients have a different genetic background to Caucasian and even other Asian patients in other countries.	24257225	Details
FAS	SNP	rs2234978	PCR	MS	Disease risk	Three SNPs linked to MS clinical severity showed a significant association between the genotype and either the proportion of active lesions (rs2234978/FAS and rs11957313/KCNIP1) or the proportion of mixed active/inactive lesions (rs8056098/CLEC16A)	This is in part because of the difficulty in the functional translation of genotype into disease-relevant mechanisms	31228212	Details
IL7R	Allele	NA	PCR	MS	Disease risk	We found reduced IL-7Ra expression on conventional T cells and upregulated IL-7 plasma levels together with reduction of RTE-Treg frequencies and Treg function in MS, without clear genetic influence. Decreased IL-7Ra expression in MS correlated with declined dual-receptor-Treg and reduced MDC TSLPR expression, indicating contracted thymic Treg output	RTE-Treg and long-lived memory Treg coincides with the MS-associated Treg defect, as shown previously. Recent studies demonstrate that IL-7 and thymic stromal lymphopoietin (TSLP) are critical for Treg matura-tion.	21287555	Details
TRB	expansion	Vβ11	PCR	MS	Disease risk	The frequency of Vβ expansion in healthy subjects and patients with MS during active and remission phasesa	immunotherapy with TCR DNA vaccines targeting Vβs selected by spectratyping analysis successfully suppressed the development of autoimmune diseases.	12707368	Details
IL4	allele	I3(2580) C	PCR	MS	Disease risk	Genotype distribution and case-control analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DRB1	polymorphism	DRB1*1201	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
ITGA4	SNP	Rs6714061	PCR	MS	Disease risk	Although this study has failed to find any associations, we suggest that further studies should fully assess the contribution of this gene to MS susceptibility.	N/A	17689671	Details
IL2RA	SNP	rs12722489	PCR	MS	Disease risk	There were no significant differences.	IL2RA genes are involved in T cell regulation which plays an important role in the pathogenesis of autoimmune diseases besides MS.Han Chinese MS and patients have a different genetic background to Caucasian and even other Asian patients in other countries.	24257225	Details
KCNIP1	SNP	rs11957313	PCR	MS	Disease risk	Three SNPs linked to MS clinical severity showed a significant association between the genotype and either the proportion of active lesions (rs2234978/FAS and rs11957313/KCNIP1) or the proportion of mixed active/inactive lesions (rs8056098/CLEC16A)	This is in part because of the difficulty in the functional translation of genotype into disease-relevant mechanisms	31228212	Details
MMEL1	SNP	rs3748816	PCR	MS	Disease risk	A combined analysis of the nsSNP screen and replication data provides evidence implicating a novel additional locus, rs3748816 in MMEL1 in multiple sclerosis susceptibilit	Several single nucleotide polymorphism (SNP) genome-wide association studies (GWAS) have been completed in multiple sclerosis.	20574445	Details
TRB	expansion	Vβ12	PCR	MS	Disease risk	The frequency of Vβ expansion in healthy subjects and patients with MS during active and remission phasesa	immunotherapy with TCR DNA vaccines targeting Vβs selected by spectratyping analysis successfully suppressed the development of autoimmune diseases.	12707368	Details
IL4	genotype	5V(-523) CC	PCR	MS	Phenotype risk	Disease course analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DRB1	polymorphism	DRB1*1202	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
ITGA4	SNP	Rs4667319	PCR	MS	Disease risk	Although this study has failed to find any associations, we suggest that further studies should fully assess the contribution of this gene to MS susceptibility.	N/A	17689671	Details
IL7R	SNP	rs6897932	PCR	MS	Disease risk	There were no significant differences.	IL7RA genes are involved in T cell regulation which plays an important role in the pathogenesis of autoimmune diseases besides MS.Han Chinese MS and patients have a different genetic background to Caucasian and even other Asian patients in other countries.	24257225	Details
CLEC16A	SNP	rs8056098	PCR	MS	Disease risk	Three SNPs linked to MS clinical severity showed a significant association between the genotype and either the proportion of active lesions (rs2234978/FAS and rs11957313/KCNIP1) or the proportion of mixed active/inactive lesions (rs8056098/CLEC16A)	This is in part because of the difficulty in the functional translation of genotype into disease-relevant mechanisms	31228212	Details
IRF5	Allele	NA	PCR	MS	Disease risk	Our preliminary study indicates that genetic variants in IRF5 may affect neither NMO nor MS in the Southeastern Han Chinese population. Further studies with a large sample size and diverse ancestry populations are needed to clarify this issue.	Neuromyelitis optica (NMO) and multiple sclerosis (MS) are demyelinating disorders of the central nervous system. Interferon regulatory factor 5 (IRF5) is a common susceptibility gene to different autoimmune disorders. However, the association of IRF5 variants with NMO and MS patients has not been well studied. Therefore, we aimed to evaluate whether IRF5 variants were associated with NMO and MS in the Southeastern Han Chinese population.	26112714	Details
TRB	expansion	Vβ13	PCR	MS	Disease risk	The frequency of Vβ expansion in healthy subjects and patients with MS during active and remission phasesa	immunotherapy with TCR DNA vaccines targeting Vβs selected by spectratyping analysis successfully suppressed the development of autoimmune diseases.	12707368	Details
IL4	genotype	5V(-523) CT	PCR	MS	Phenotype risk	Disease course analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DRB1	polymorphism	DRB1*1301	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
CCL2	SNP	-2138A>T	PCR	MS	Disease risk	We also identified marginally significant (uncorrected) transmission distortion for haplotypes encompassing the CCL2 genes.	CC chemokines chemoattract a wide range of cells, including lymphocytes, dendritic cells, monocytes and some granulocytes, whilst CXC chemokines are chemoattractant for neutrophils and lymphocytes. There is increasing evidence for chemokines possessing abilities beyond that of migration, including T-helper cell subset differentiation, T cell costimulation, and macrophage and natural killer cell maturation .Substantial evidence supports the involvement of CC chemokines in the pathogenesis of MS.	16872505	Details
MOG	SNP	rs3130253	PCR	MS	Disease risk	Three SNPs linked to MS pathology-associated genes showed a significant association with either proportion of active lesions (rs3130253/MOG), incidence of cortical gray matter lesions (rs1064395/NCAN) or the proportion of remyelinated lesions (rs5742909/CTLA4)	This is in part because of the difficulty in the functional translation of genotype into disease-relevant mechanisms	31228212	Details
IL7R	Allele	NA	PCR	MS	Treatment risk	In conclusion, our findings suggest that IL-7Ra polymorphisms can influence T cell development and homeostasis, and thereby contribute to the altered immune regulation associated with disease development in patients with MS	The receptor for the homeostatic T cell cytokine interleukin-7 (IL-7Ra) has recently shown genetic association to multiple sclerosis (MS).	20072142	Details
TRB	expansion	Vβ14	PCR	MS	Disease risk	The frequency of Vβ expansion in healthy subjects and patients with MS during active and remission phasesa	immunotherapy with TCR DNA vaccines targeting Vβs selected by spectratyping analysis successfully suppressed the development of autoimmune diseases.	12707368	Details
IL4	genotype	5V(-523) TT	PCR	MS	Phenotype risk	Disease course analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DRB1	polymorphism	DRB1*1302	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
AQP4	SNP	rs16942851, rs1058424, rs335929, rs335931, rs162007, rs3763043	PCR	MS	Disease risk	This study showed no significant association of common AQP4 SNPs with MS, strongly suggesting that polymorphisms of AQP4 gene are unlikely to confer MS susceptibility, at least in Northern Han Chinese population.	Unlike NMO, various genetic and environmental factors contribute to etiology of MS. AQP4, expressed in astrocytes in the brain, spinal cord, optic nerve and supportive cells in sensory organs, is the most abundantly distributed water channel in CNS.	28123825	Details
CCL11	SNP	-488C>A	PCR	MS	Disease risk	We also identified marginally significant (uncorrected) transmission distortion for haplotypes encompassing the CCL11 genes.	CC chemokines chemoattract a wide range of cells, including lymphocytes, dendritic cells, monocytes and some granulocytes, whilst CXC chemokines are chemoattractant for neutrophils and lymphocytes. There is increasing evidence for chemokines possessing abilities beyond that of migration, including T-helper cell subset differentiation, T cell costimulation, and macrophage and natural killer cell maturation .Substantial evidence supports the involvement of CC chemokines in the pathogenesis of MS.	16872505	Details
NCAN	SNP	rs1064395	PCR	MS	Disease risk	Three SNPs linked to MS pathology-associated genes showed a significant association with either proportion of active lesions (rs3130253/MOG), incidence of cortical gray matter lesions (rs1064395/NCAN) or the proportion of remyelinated lesions (rs5742909/CTLA4)	This is in part because of the difficulty in the functional translation of genotype into disease-relevant mechanisms	31228212	Details
IL10	Allele	NA	PCR	MS	Disease risk	Genotype frequencies for all the analyzed polymorphisms were not differently distributed between cases and controls.	Multiple sclerosis (MS) is a cell-mediated autoimmune dis-ease characterized by type-1 cytokine production.	16803996	Details
SOCS1	SNP	rs243324	PCR	MS	Disease risk	There were no significant differences in the genotype frequencies of SOCS1 rs243324 SNP between MS patients and the healthy controls. Moreover, the rs243324 SNP did not affect the expression level of SOCS1 mRNA in PBMCs of RR-MS patients	SOCS1 regulates the signaling of cytokines via JAK–STAT pathway	25701091	Details
TRB	expansion	Vβ15	PCR	MS	Disease risk	The frequency of Vβ expansion in healthy subjects and patients with MS during active and remission phasesa	immunotherapy with TCR DNA vaccines targeting Vβs selected by spectratyping analysis successfully suppressed the development of autoimmune diseases.	12707368	Details
IL4	allele	5V(-523) C	PCR	MS	Phenotype risk	We screened the promoter region, exons 1 – 4 and their splice sites for polymorphisms and tested the association between novel polymorphisms E1(33)*C ! T and I3(2580)*C ! A, and the established 5V( 523)*C ! T and I3(709)*VNTR polymorphisms with susceptibility to, age of onset in, and course and severity of MS in sporadic cases.	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DRB1	polymorphism	DRB1*1401	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
CCR5	allele	Δ32	PCR	MS	Disease risk	The frequencies of CCR5Δ32 alleles in patients with MS did not differ significantly from those of controls and were not influenced by gender. We did not observed any significant association between CCR5Δ32 allele and age onset.	Genetic studies indicate that CC-chemokines and chemokine receptors are involved in the susceptibility to MS, in fact;they play a significant role in the migration of monocytes and T cells.A nonfunctional allele, resulting from a 32-bp deletion in exon 4, CCR5Δ32, leads to a truncated form of the functional receptor.Moreover, in the CNS, CCR5 is expressed on neurons, astrocytes, and microglia, as well as on endothelium and vascular smooth muscle cells and on T-helper cells.During MS pathogenesis, the absence of functional CCR5 on the cell surface could lead to reduced trafficking of leucocytes into the lesion sites, thus downregulating inflammation in brain tissue.	22096627	Details
IL6	polymorphism	C allele present or absent	PCR	MS	Disease risk	There were no differences in the allelic distribution of the IL-6 gene C allele between MS patients and healthy controls.	A dysregulation of IL-6 might contribute to MS pathogenesis.	11072134	Details
CTLA4	SNP	rs5742909	PCR	MS	Disease risk	Three SNPs linked to MS pathology-associated genes showed a significant association with either proportion of active lesions (rs3130253/MOG), incidence of cortical gray matter lesions (rs1064395/NCAN) or the proportion of remyelinated lesions (rs5742909/CTLA4)	This is in part because of the difficulty in the functional translation of genotype into disease-relevant mechanisms	31228212	Details
IL-12	Allele	NA	PCR	MS	Disease risk	Genotype frequencies for all the analyzed polymorphisms were not differently distributed between cases and controls.	Multiple sclerosis (MS) is a cell-mediated autoimmune dis-ease characterized by type-1 cytokine production.	16803996	Details
VAMP2	polymorphisms	N/A	PCR	MS	Disease risk	we reanalyse public ChIP-seq and RNA-seq data to classify VSEs into three categories according to their combinations of persistent and secondary VDR binding. Secondly, we indicate the genes with VSE regions that are near MS risk variants. Furthermore, we find that MS risk variants are enriched in VSE regions, and we indicate some genes with a VSE overlapping MS risk variant for further exploration. We also find two clusters of genes from the set of genes showing correlation of expression patterns with the MS risk gene ZMIZ1 that appear to be regulated by VSEs in THP-1 cell	transcription factor (TF) binding regions	30941131	Details
TRB	expansion	Vβ16	PCR	MS	Disease risk	The frequency of Vβ expansion in healthy subjects and patients with MS during active and remission phasesa	immunotherapy with TCR DNA vaccines targeting Vβs selected by spectratyping analysis successfully suppressed the development of autoimmune diseases.	12707368	Details
IL4	allele	5V(-523) T	PCR	MS	Phenotype risk	Disease course analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DRB1	polymorphism	DRB1*1403	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
HLA-DRB1	polymorphisms	DRB1*15:01	PCR	MS	Disease risk	The following major histocompatibility complex risk alleles were replicated: HLADRB1*15:01, HLA-DRB1*03:01, as well as HLA-DRB1*04:05 and the African-specific risk allele of HLA-DRB1*15:03.	N/A	23771490	Details
FAS	SNP	rs2234978	PCR	MS	Disease risk	rs2234978/FAS T-allele carriers showed increased FAS gene expression levels in perivascular T cells and perilesional oligodendrocytes	This is in part because of the difficulty in the functional translation of genotype into disease-relevant mechanisms	31228212	Details
TNF	Allele	NA	PCR	MS	Disease risk	Genotype frequencies for all the analyzed polymorphisms were not differently distributed between cases and controls.	Multiple sclerosis (MS) is a cell-mediated autoimmune dis-ease characterized by type-1 cytokine production.	16803996	Details
TREM2	SNP	rs75932628	PCR	MS	Disease risk	Minor allele rs75932628-T frequency was reported between 0.0017 to 0.003 in European populations	TREM2 is a signaling protein which participates in the innate immune system by implication to inflammation, proliferation and phagocytosis.	31362167	Details
TRB	expansion	Vβ17	PCR	MS	Disease risk	The frequency of Vβ expansion in healthy subjects and patients with MS during active and remission phasesa	immunotherapy with TCR DNA vaccines targeting Vβs selected by spectratyping analysis successfully suppressed the development of autoimmune diseases.	12707368	Details
IL4	genotype	E1(33) CC	PCR	MS	Phenotype risk	We screened the promoter region, exons 1 – 4 and their splice sites for polymorphisms and tested the association between novel polymorphisms E1(33)*C ! T and I3(2580)*C ! A, and the established 5V( 523)*C ! T and I3(709)*VNTR polymorphisms with susceptibility to, age of onset in, and course and severity of MS in sporadic cases.	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DRB1	polymorphism	DRB1*1405	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
HLA-DRB1	polymorphisms	DRB1*03:01	PCR	MS	Disease risk	The following major histocompatibility complex risk alleles were replicated: HLADRB1*15:01, HLA-DRB1*03:01, as well as HLA-DRB1*04:05 and the African-specific risk allele of HLA-DRB1*15:03.	N/A	23771490	Details
HLA-DRB1	Allele	NA	PCR	MS	Disease risk	Our study confirms that the risk effects attributable to the HLA- DRB1*15:01and DRB1*03 alleles seen in Europeans are also seen in Indians. The absence of any evidence of association with DQB1 alleles reflects the lower linkage disequilibrium between DQB1 alleles and DRB1 risk alleles present in this population, and illustrates the potential value of fine mapping signals of association in different ethnic groups.	Previous efforts to identify Human Leukocyte Antigen (HLA) gene associations with mul-tiple sclerosis (MS) in the South Asian population have been underpowered.	25921049	Details
TRB	expansion	Vβ18	PCR	MS	Disease risk	The frequency of Vβ expansion in healthy subjects and patients with MS during active and remission phasesa	immunotherapy with TCR DNA vaccines targeting Vβs selected by spectratyping analysis successfully suppressed the development of autoimmune diseases.	12707368	Details
IL4	genotype	E1(33) TT	PCR	MS	Phenotype risk	Disease course analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DRB1	polymorphism	DRB1*1406	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
HLA-DRB1	polymorphisms	DRB1*04:05	PCR	MS	Disease risk	The following major histocompatibility complex risk alleles were replicated: HLADRB1*15:01, HLA-DRB1*03:01, as well as HLA-DRB1*04:05 and the African-specific risk allele of HLA-DRB1*15:03.	N/A	23771490	Details
HLA-DQB1	Allele	NA	PCR	MS	Disease risk	Our study confirms that the risk effects attributable to the HLA- DRB1*15:01and DRB1*03 alleles seen in Europeans are also seen in Indians. The absence of any evidence of association with DQB1 alleles reflects the lower linkage disequilibrium between DQB1 alleles and DRB1 risk alleles present in this population, and illustrates the potential value of fine mapping signals of association in different ethnic groups.	Previous efforts to identify Human Leukocyte Antigen (HLA) gene associations with mul-tiple sclerosis (MS) in the South Asian population have been underpowered.	25921049	Details
APOE	epsilon-4 allele	N/A	PCR	MS	N/A	Our results do not suggest any association between the presence of the ApoE epsilon-4 allele and the progression of disability in patients with MS in our sample.	N/A	20073019	Details
TRB	expansion	Vβ19	PCR	MS	Disease risk	The frequency of Vβ expansion in healthy subjects and patients with MS during active and remission phasesa	immunotherapy with TCR DNA vaccines targeting Vβs selected by spectratyping analysis successfully suppressed the development of autoimmune diseases.	12707368	Details
IL4	genotype	E1(33) CT	PCR	MS	Phenotype risk	Disease course analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DRB1	polymorphism	DRB1*0701	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
HLA-DRB1	polymorphisms	DRB1*15:03	PCR	MS	Disease risk	The following major histocompatibility complex risk alleles were replicated: HLADRB1*15:01, HLA-DRB1*03:01, as well as HLA-DRB1*04:05 and the African-specific risk allele of HLA-DRB1*15:03.	N/A	23771490	Details
TNF	allele	N/A	PCR	MS	Disease risk	There were no statistically significant differences between the TNF2 allelic frequencies in the groups of patients with MS.	Tumor necrosis factor alpha (TNFa) is a proinflammatory cytokine produced by the TH1 subset of T-helper lymphocytes. It has been implicated in the pathogenesis and course of several immunemediated diseases, including MS.	9270614	Details
IL1B	SNP	rs35829419	PCR	MS、EAE	Disease risk	Altogether, these results point to a role of IL1B and the NLRP3 inflammasome as prognostic biomarker and potential therapeutic target, respectively, in patients with primary progressive multiple sclerosis.	NF-jB pathway	32282893	Details
TRB	expansion	Vβ20	PCR	MS	Disease risk	The frequency of Vβ expansion in healthy subjects and patients with MS during active and remission phasesa	immunotherapy with TCR DNA vaccines targeting Vβs selected by spectratyping analysis successfully suppressed the development of autoimmune diseases.	12707368	Details
IL4	allele	E1(33) C	PCR	MS	Phenotype risk	Disease course analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
LTA	polymorphisms	TNF-β NcoI	PCR	MS	Disease risk	The TNFB2/B2 genotype of TNF-β NcoI polymorphism was associated with increased inflammatory and metabolic markers and this association was different according to sex of MS patients.	N/A	25173940	Details
HLA-DRB1	polymorphism	DRB1*0802	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
HLA-DRB1	polymorphisms	DRB1*11:01	PCR	MS	Disease risk	The following major histocompatibility complex risk alleles were replicated: HLADRB1*15:01, HLA-DRB1*03:01, as well as HLA-DRB1*04:05 and the African-specific risk allele of HLA-DRB1*15:03.	N/A	23771490	Details
SERPINA1	allele	M3	PCR	MS	Disease risk	There was an increase over controls in the number of patients with phenotypes containing M3, and the gene frequency of M3 is significantly increased over controls.The proportion of patients with the M3 gene is significantly higher than in the control population.	Alpha-1 Antitrypsin, the major circulating protease inhibitor, has more than thirty alleles. In addition to its role as a protease inhibitor, alpha-1 antitrypsin may regulate the immune response. As there is evidence that both the inflammatory polyneuropathies and multiple sclerosis have an immune basis, and that genetic factors influence susceptibility.	3878126	Details
IL1RL1	SNP	rs1041973	PCR	MS	Disease risk	Our study showed that IL1RAP rs4624606, IL-6 rs1800795, and HTRA1 rs11200638 are not associated with an increased risk of developing ON. However, the IL1RL1 rs1041973 A/C genotype might be associated with an increased risk of developing ON.	The aim of our study was to determine the associations between IL1RAP rs4624606, IL1RL1 rs1041973,IL-6 rs1800795, and HTRA1 rs11200638 gene polymorphisms and development of ON with or without MS.	32449403	Details
HHEX	SNP	rs7923837	PCR	MS	Disease risk	The present study evidenced statistically significant lower HHEX mRNA levels in lymphocytes of MS patients compared to those of controls, showing a similar trend in MS patients to the already described eQTL effect in blood from healthy individuals. Even though no differences were found in protein expression according to HHEX genotypes, statistically significant divergent subcellular distributions of HHEX appeared in patients and controls. The epistatic interaction detected between BCL6 and HHEX MS-risk variants in healthy individuals was absent in patients, indicative of a perturbed reciprocal regulation in the latter. Lymphocytes from MS carriers of the homozygous mutant genotype exhibited a distinctive, more energetic profile, both in resting and activated conditions, and significantly increased glycolytic rates in resting conditions when compared to controls sharing the HHEX genotype. In contrast, significantly higher mitochondrial mass was evidenced in homozygous mutant controls.	eIF4E-mediated mRNA transport	35887298	Details
TRB	expansion	Vβ21	PCR	MS	Disease risk	The frequency of Vβ expansion in healthy subjects and patients with MS during active and remission phasesa	immunotherapy with TCR DNA vaccines targeting Vβs selected by spectratyping analysis successfully suppressed the development of autoimmune diseases.	12707368	Details
IL4	allele	E1(33) T	PCR	MS	Phenotype risk	We screened the promoter region, exons 1 – 4 and their splice sites for polymorphisms and tested the association between novel polymorphisms E1(33)*C ! T and I3(2580)*C ! A, and the established 5V( 523)*C ! T and I3(709)*VNTR polymorphisms with susceptibility to, age of onset in, and course and severity of MS in sporadic cases.	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DRB1	polymorphism	DRB1*0803	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
HLA-DRB1	polymorphisms	DRB1*04:01:01	PCR	MS	Disease risk	The following major histocompatibility complex risk alleles were replicated: HLADRB1*15:01, HLA-DRB1*03:01, as well as HLA-DRB1*04:05 and the African-specific risk allele of HLA-DRB1*15:03.	N/A	23771490	Details
IL1RAP	SNP	rs4624606	PCR	MS	Disease risk	Our study showed that IL1RAP rs4624606, IL-6 rs1800795, and HTRA1 rs11200638 are not associated with an increased risk of developing ON. However, the IL1RL1 rs1041973 A/C genotype might be associated with an increased risk of developing ON.	The aim of our study was to determine the associations between IL1RAP rs4624606, IL1RL1 rs1041973,IL-6 rs1800795, and HTRA1 rs11200638 gene polymorphisms and development of ON with or without MS.	32449403	Details
CCR5	A 32-bp deletion in the CCR5	N/A	PCR	MS	Disease risk	Progression to disability was prolonged in Delta32CCR5 homozygotes and heterozygotes compared with MS patients with the CCR5 wild-type genotype (p < 0.005). Mutated CCR5 allele may be considered a favorable prognostic factor in MS.	The current findings, taken together with increased expression of CCR5 on circulating T cells in MS patients compared with healthy control subjects,the aberrant migration of MS-derived T cells toward RANTES and MIP-1 due to overexpression of their CCR5 receptors,and the increase in CCR5+ circulating CD4+cells during acute MS relapses,suggest that CCR5 antagonists could be considered a potential target for therapeutic intervention in MS.	12874407	Details
WAS	altering histone methylation	N/A	PCR	EAE	Treatment risk	The main purpose of this study is to identify potential regulatory elements in CBD-mediated immune modulation.	CBD suppresses inflammation through multiple mechanisms	31673072	Details
TRB	expansion	Vβ22	PCR	MS	Disease risk	The frequency of Vβ expansion in healthy subjects and patients with MS during active and remission phasesa	immunotherapy with TCR DNA vaccines targeting Vβs selected by spectratyping analysis successfully suppressed the development of autoimmune diseases.	12707368	Details
IL4	genotype	E1(33)	PCR	MS	Phenotype risk	Disease course analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DRB1	polymorphism	DRB1*0901	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
HLA-DRB1	polymorphisms	DRB1*16:02	PCR	MS	Disease risk	The following major histocompatibility complex risk alleles were replicated: HLADRB1*15:01, HLA-DRB1*03:01, as well as HLA-DRB1*04:05 and the African-specific risk allele of HLA-DRB1*15:03.	N/A	23771490	Details
VDR	SNP	rs2225870	PCR	MS	Disease risk	Distribution of Fok-I polymorphisms in the MS and control groups differ significantly in dominant, heterozygote, and homozygote inheritance models.There were significant differences of Fok-I polymorphism allele frequencies across MS/MS subtype group and the control group.	Variants in the vitamin D receptor (VDR) gene affect MS susceptibility by the way of changing the interaction of VDRE on the MHC regulatory region. Several studies indicate that the VDR gene polymorphisms are associated with susceptibility to MS. Furthermore, these polymorphisms in the VDR gene may change the vitamin D serum levels, vitamin D structure, and function as such with an immune modulatory effect; these are the mechanisms of the vitamin D and VDR complex.	36880035	Details
MMP9	promoter polymorphism	MMP-9 PM ≥22 CA	PCR	MS	Disease risk	Comparison of allelic frequencies showed that a higher number of CA repeats characterized the MS group ( P< 0.0001) and prevalence of carriers of z22 CA repeats was higher in the MS than in the Control Group	N/A	15223247	Details
IL6	SNP	rs1800795	PCR	MS	Disease risk	Our study showed that IL1RAP rs4624606, IL-6 rs1800795, and HTRA1 rs11200638 are not associated with an increased risk of developing ON. However, the IL1RL1 rs1041973 A/C genotype might be associated with an increased risk of developing ON.	The aim of our study was to determine the associations between IL1RAP rs4624606, IL1RL1 rs1041973,IL-6 rs1800795, and HTRA1 rs11200638 gene polymorphisms and development of ON with or without MS.	32449403	Details
TAC1	SNP	rs1510303	PCR	MS	Disease risk	Two-marker haplotypes composed of allelic combinations of TAC1 promoter–intron 1 SNPs were highly significantly associated with MS and more so with the relapsing-remitting form of this disease. While independent reproduction of these data in other data sets is indicated, our work is suggestive for a role of the TAC1 gene in MS	AC1 promoter–intron 1 SNPs	15729363	Details
TRB	expansion	Vβ23	PCR	MS	Disease risk	The frequency of Vβ expansion in healthy subjects and patients with MS during active and remission phasesa	immunotherapy with TCR DNA vaccines targeting Vβs selected by spectratyping analysis successfully suppressed the development of autoimmune diseases.	12707368	Details
IL4	genotype	I3(709) 11	PCR	MS	Phenotype risk	Disease course analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
HLA-DRB1	polymorphism	DRB1*1001	PCR	MS	Disease risk	HLA alleles may correlate with risk for MS together with VDRG.	N/A	10967184	Details
HLA-DRB1	polymorphisms	DRB1*14:01	PCR	MS	Disease risk	The following major histocompatibility complex risk alleles were replicated: HLADRB1*15:01, HLA-DRB1*03:01, as well as HLA-DRB1*04:05 and the African-specific risk allele of HLA-DRB1*15:03.	N/A	23771490	Details
VDR	SNP	rs1544410	PCR	MS	Disease risk	There was no significant difference in Bsm-I polymorphism genotype distribution across MS/MS subtype group and the control group in any inheritance models.	Variants in the vitamin D receptor (VDR) gene affect MS susceptibility by the way of changing the interaction of VDRE on the MHC regulatory region. Several studies indicate that the VDR gene polymorphisms are associated with susceptibility to MS. Furthermore, these polymorphisms in the VDR gene may change the vitamin D serum levels, vitamin D structure, and function as such with an immune modulatory effect; these are the mechanisms of the vitamin D and VDR complex.	36880035	Details
HLA-DRB1	allele	HLA-DRB1*15	PCR	MS	Disease risk	No single allele is associated with either a good or poor prognosis	N/A	10426152	Details
HTRA1	SNP	rs11200638	PCR	MS	Disease risk	Our study showed that IL1RAP rs4624606, IL-6 rs1800795, and HTRA1 rs11200638 are not associated with an increased risk of developing ON. However, the IL1RL1 rs1041973 A/C genotype might be associated with an increased risk of developing ON.	The aim of our study was to determine the associations between IL1RAP rs4624606, IL1RL1 rs1041973,IL-6 rs1800795, and HTRA1 rs11200638 gene polymorphisms and development of ON with or without MS.	32449403	Details
SH2D2A	SH2D2A GA repeat	N/A	PCR	MS	N/A	No linkage or association of MS to four genetic markers flanking the SH2D2A gene was observed.	Since the SH2D2A protein modulates T cell activation, this may be a mechanism for how short SH2D2A alleles confer susceptibility to develop MS.	11528519	Details
PRKCA	SNP	rs7220007	PCR	MS	Disease risk	The transcript levels of PRKCA showed correlation with the copy number of the Finnish and Canadian ‘‘risk’’ haplotypes in CD4-negative mononuclear cells of five Finnish multiplex families and in lymphoblast cell lines of 11 Centre d’Etude du Polymorphisme Humain (CEPH) individuals of European origin	PKC	16596167	Details
TRB	expansion	Vβ24	PCR	MS	Disease risk	The frequency of Vβ expansion in healthy subjects and patients with MS during active and remission phasesa	immunotherapy with TCR DNA vaccines targeting Vβs selected by spectratyping analysis successfully suppressed the development of autoimmune diseases.	12707368	Details
IL4	genotype	I3(709) 12	PCR	MS	Phenotype risk	Disease course analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
RGS1	SNP	rs2760524	PCR	MS	Disease risk	No SNP was associated with systematic deflection in time to disability milestones, age at onset or time to secondary progression.	N/A	22732448	Details
HLA-DRB1	polymorphisms	DRB1*09:01	PCR	MS	Disease risk	The following major histocompatibility complex risk alleles were replicated: HLADRB1*15:01, HLA-DRB1*03:01, as well as HLA-DRB1*04:05 and the African-specific risk allele of HLA-DRB1*15:03.	N/A	23771490	Details
VDR	SNP	rs731236	PCR	MS	Disease risk	Distribution of Taq-I polymorphisms in the MS and control groups differ significantly in dominant, heterozygote, and homozygote inheritance models.There were significant differences of Taq-I polymorphism allele frequencies across MS/MS subtype group and the control group.	Variants in the vitamin D receptor (VDR) gene affect MS susceptibility by the way of changing the interaction of VDRE on the MHC regulatory region. Several studies indicate that the VDR gene polymorphisms are associated with susceptibility to MS. Furthermore, these polymorphisms in the VDR gene may change the vitamin D serum levels, vitamin D structure, and function as such with an immune modulatory effect; these are the mechanisms of the vitamin D and VDR complex.	36880035	Details
HLA-DRB1	allele	HLA-DRB1*04	PCR	MS	Disease risk	No single allele is associated with either a good or poor prognosis	N/A	10426152	Details
GFI1	SNP	rs11804321	PCR	MS	Disease risk	This Tag-SNP captures two SNPs in complete linkage disequilibrium (r21), both located within the 17th intron of the EVI5 gene. Our findings agree with the corresponding data of the recent IMSGC study and present new genetic evidence that points to EVI5 as a factor of susceptibility to MS	We observed an association with MS in three of eight Tag-SNPs: rs11804321 (P0.008, OR1.29; 95% CI1.08–1.54), rs11808092 (P0.048, OR1.19; 95% CI1.03–1.39) and rs6680578 (P0.0082, OR1.23; 95% CI1.07–1.41)	20087403	Details
Spp1	SNP	rs 4754	PCR	MS	Disease risk	The four SNPs finally considered in our analysis include two located in coding regions of the osteopontin gene and two from non-coding regions of exon 7. Although none of these variations lead to amino-acid changes they may still be functionally important by altering mRNA stability or localization or be in linkage disequilibrium with functionally important variants located in other parts of the osteopontin gene	After typing the first 286 affected and 192 control individuals, heterozygosity rates for the SNPs were examined. No heterozygous individuals were identified for SNPs 3 and 5 and heterozygosity rates for SNPs 7 and 8 were less than 5 % in cases and controls.These four SNPs were therefore dropped from the study and only SNPs 1, 2, 4 and 6 were used to complete the analysis	12928913	Details
IL4	genotype	I3(709) 22	PCR	MS	Phenotype risk	Disease course analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
KIF21B	SNP	rs12122721	PCR	MS	Disease risk	No SNP was associated with systematic deflection in time to disability milestones, age at onset or time to secondary progression.	The details of KIF21B’s functions are not well understood, but it may be relevant for maintenance of axonal integrity.	22732448	Details
HLA-DRB1	polymorphisms	DRB1*08:04	PCR	MS	Disease risk	The following major histocompatibility complex risk alleles were replicated: HLADRB1*15:01, HLA-DRB1*03:01, as well as HLA-DRB1*04:05 and the African-specific risk allele of HLA-DRB1*15:03.	N/A	23771490	Details
CD40	polymorphism	C/T	PCR	MS	Disease risk	No significant differences were found in the frequency of the C/T(-1) polymorphism between the patients with MS and the controls or among different MS subtypes.	The cell surface receptor CD40, a member of the tumor necrosis factor receptor family, is expressed on all nonterminally differentiated B cells and plays a fundamental role in B-cell activation and in regulation of adaptive immune responses.T allele results in a diminished expression of CD40 in an in vitro transcription/translation system and that the C/T CD40 polymorphism acts at the level of gene translation, modulating B-cell–T-cell interactions in autoimmune reactions by affecting expression of the CD40 protein.	17026470	Details
TRBV20OR9-2	Gene Polymorphism	BV2S1	PCR	MS	Disease risk	these results suggest that it is unlikely that germ-line polymorphism in the TCRBV locus makes a major contribution to MS susceptibility	No significant differences in allele, genotype, or phenotype frequencies were observed between the MS patients and controls for any of the 14 TCRBV-gene polymorphisms studied	7717407	Details
GFI1	SNP	rs11808092	PCR	MS	Disease risk	This Tag-SNP captures two SNPs in complete linkage disequilibrium (r21), both located within the 17th intron of the EVI5 gene. Our findings agree with the corresponding data of the recent IMSGC study and present new genetic evidence that points to EVI5 as a factor of susceptibility to MS	We observed an association with MS in three of eight Tag-SNPs: rs11804321 (P0.008, OR1.29; 95% CI1.08–1.54), rs11808092 (P0.048, OR1.19; 95% CI1.03–1.39) and rs6680578 (P0.0082, OR1.23; 95% CI1.07–1.41)	20087403	Details
ERG	DNA methylation	N/A	PCR	MS	Disease risk	ERG polymorphism should whereas in the late-stage pregnancy group, no difference in be further studied in other populations to obtain more BMD was shown in XbaI polymorphism. The Xx genotype adequate strategies for treatment of MS.	After informed consent was obtained from each subject, and human leukocyte antigens (HLA). high-molecular weight DNA was extracted from their peripheral blood cells. Polymerase chain reaction (PCR) amplification was performed on the region containing the PvuII and XbaI polymorphisms	11054488	Details
IL4	allele	I3(709) 1	PCR	MS	Phenotype risk	Disease course analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
TMEM39A	SNP	rs1132200	PCR	MS	Disease risk	No SNP was associated with systematic deflection in time to disability milestones, age at onset or time to secondary progression.	N/A	22732448	Details
HLA-DRB1	polymorphisms	DRB1*11:02	PCR	MS	Disease risk	The following major histocompatibility complex risk alleles were replicated: HLADRB1*15:01, HLA-DRB1*03:01, as well as HLA-DRB1*04:05 and the African-specific risk allele of HLA-DRB1*15:03.	N/A	23771490	Details
TRBV20OR9-2	Gene Polymorphism	BV3S1	PCR	MS	Disease risk	germ-line polymorphism in the TCRBV locus makes a major contribution to MS susceptibility	No significant differences in allele, genotype, or phenotype frequencies were observed between the MS patients and controls for any of the 15 TCRBV-gene polymorphisms studied	7717407	Details
GFI1	SNP	rs6680578	PCR	MS	Disease risk	This Tag-SNP captures two SNPs in complete linkage disequilibrium (r21), both located within the 17th intron of the EVI5 gene. Our findings agree with the corresponding data of the recent IMSGC study and present new genetic evidence that points to EVI5 as a factor of susceptibility to MS	We observed an association with MS in three of eight Tag-SNPs: rs11804321 (P0.008, OR1.29; 95% CI1.08–1.54), rs11808092 (P0.048, OR1.19; 95% CI1.03–1.39) and rs6680578 (P0.0082, OR1.23; 95% CI1.07–1.41)	20087403	Details
HLA-DRB1	restriction fragment length polymorphism	N/A	PCR	MS	Disease risk	Pooled DNA from Scottish DR2-positive individuals digested with Mspl and probed with HLADQc~, showing the presence of a 3.25-kb fragment in MS patients (A) but not in healthy unrelated controls (B)	The use of DNA pooled from groups of patients and controls from northeast Scotland enabled the screening of 14 restriction endonucleases with five HLA-D region probes (DPa, DPB, DQa, DQRB) and two T-cell antigen receptor probes	2567726	Details
IL4	allele	I3(709) 2	PCR	MS	Phenotype risk	Disease course analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
IL7R	SNP	rs6897932	PCR	MS	Disease risk	No SNP was associated with systematic deflection in time to disability milestones, age at onset or time to secondary progression.	N/A	22732448	Details
HLA-DRB1	polymorphisms	DRB1*07:01	PCR	MS	Disease risk	The following major histocompatibility complex risk alleles were replicated: HLADRB1*15:01, HLA-DRB1*03:01, as well as HLA-DRB1*04:05 and the African-specific risk allele of HLA-DRB1*15:03.	N/A	23771490	Details
TRBV20OR9-2	Gene Polymorphism	BV6S5	PCR	MS	Disease risk	germ-line polymorphism in the TCRBV locus makes a major contribution to MS susceptibility	No significant differences in allele, genotype, or phenotype frequencies were observed between the MS patients and controls for any of the 16 TCRBV-gene polymorphisms studied	7717407	Details
NFKB1	Allele	NA	PCR	MS	Disease risk	The genes of NF?B inhibitors exhibit more sequence variations. In the IKBL gene a predisposing allele was identified (13.1% vs 7.5% in the control group, P ? 0.001).	Multiple sclerosis (MS) is an autoimmune disease displaying different clinical courses. In this multifactorial disease complex environmental as well as genetic predisposition factors contribute to the disease manifestation.	12058256	Details
HLA-DQA1	restriction fragment length polymorphism	N/A	PCR	MS	Disease risk	Following digestion with MsP1 a 3.25-kb fragment was present in the MS DR2-positive pool but absent in the control DR2-positive pool	The use of DNA pooled from groups of patients and controls from northeast Scotland enabled the screening of 14 restriction endonucleases with five HLA-D region probes (DPa, DPB, DQa, DQRB) and two T-cell antigen receptor probes	2567726	Details
IL4	genotype	I3(2580) CC	PCR	MS	Phenotype risk	Disease course analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
IL2RA	SNP	rs2104286	PCR	MS	Disease risk	No SNP was associated with systematic deflection in time to disability milestones, age at onset or time to secondary progression.	N/A	22732448	Details
HLA-DRB1	polymorphisms	DRB1*13:03	PCR	MS	Disease risk	The following major histocompatibility complex risk alleles were replicated: HLADRB1*15:01, HLA-DRB1*03:01, as well as HLA-DRB1*04:05 and the African-specific risk allele of HLA-DRB1*15:03.	N/A	23771490	Details
TRBV20OR9-2	Gene Polymorphism	BV8S1	PCR	MS	Disease risk	germ-line polymorphism in the TCRBV locus makes a major contribution to MS susceptibility	No significant differences in allele, genotype, or phenotype frequencies were observed between the MS patients and controls for any of the 17 TCRBV-gene polymorphisms studied	7717407	Details
RELA	Allele	NA	PCR	MS	Disease risk	The genes of NF?B inhibitors exhibit more sequence variations. In the IKBL gene a predisposing allele was identified (13.1% vs 7.5% in the control group, P ? 0.001).	Multiple sclerosis (MS) is an autoimmune disease displaying different clinical courses. In this multifactorial disease complex environmental as well as genetic predisposition factors contribute to the disease manifestation.	12058256	Details
HLA-DQB1	restriction fragment length polymorphism	N/A	PCR	MS	Disease risk	DQB RFLP differences between DR2-negative MS and control pools. As with DQB, the majority of restriction enzymes gave rise to DQB-hybridizing restriction fragments which were identical in each of the four pools	The use of DNA pooled from groups of patients and controls from northeast Scotland enabled the screening of 14 restriction endonucleases with five HLA-D region probes (DPa, DPB, DQa, DQRB) and two T-cell antigen receptor probes	2567726	Details
IL4	genotype	I3(2580) CA	PCR	MS	Phenotype risk	Disease course analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
CLEC16A	SNP	rs12708716	PCR	MS	Disease risk	No SNP was associated with systematic deflection in time to disability milestones, age at onset or time to secondary progression.	rs12708716 is located in the CLEC16Agene, whose functionisunknown.	22732448	Details
HLA-DRB1	polymorphisms	DRB1*01:02	PCR	MS	Disease risk	The following major histocompatibility complex risk alleles were replicated: HLADRB1*15:01, HLA-DRB1*03:01, as well as HLA-DRB1*04:05 and the African-specific risk allele of HLA-DRB1*15:03.	N/A	23771490	Details
TRBV20OR9-2	Gene Polymorphism	BV8S2	PCR	MS	Disease risk	germ-line polymorphism in the TCRBV locus makes a major contribution to MS susceptibility	No significant differences in allele, genotype, or phenotype frequencies were observed between the MS patients and controls for any of the 18 TCRBV-gene polymorphisms studied	7717407	Details
CLEC16A	SNP	rs2903692	PCR	MS	Disease risk	Associations of CLEC16A polymorphisms with T1D and MS were successfully replicated in a Spanish population. A novel association of rs6498169 with a predisposition to RA was described which is consistent with previous MHC2TA results. These data provide evidence for the influence of variants within this chromosomal region on the development of complex diseases.	Genome-wide studies have identified the chromosomal region 16p13 in the susceptibility to type 1 diabetes (T1D) and multiple sclerosis (MS).	19221398	Details
HLA-DPA1	restriction fragment length polymorphism	N/A	PCR	MS	Disease risk	No polymorphism discriminating between MS and control pools was seen using DRB, DPa, DPB, TcRa, orTcRB geneprobes	The use of DNA pooled from groups of patients and controls from northeast Scotland enabled the screening of 14 restriction endonucleases with five HLA-D region probes (DPa, DPB, DQa, DQRB) and two T-cell antigen receptor probes	2567726	Details
IL4	genotype	I3(2580) AA	PCR	MS	Phenotype risk	Disease course analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
CLEC16A	SNP	rs6498169	PCR	MS	Disease risk	No SNP was associated with systematic deflection in time to disability milestones, age at onset or time to secondary progression.	However,the other SNP located in CLEC16A that we tested, rs6498169, was not associated with any phenotypic features so this may be a chance finding.	22732448	Details
HLA-DRB1	polymorphisms	DRB1*03:02	PCR	MS	Disease risk	The following major histocompatibility complex risk alleles were replicated: HLADRB1*15:01, HLA-DRB1*03:01, as well as HLA-DRB1*04:05 and the African-specific risk allele of HLA-DRB1*15:03.	N/A	23771490	Details
HLA-DRB1	allele	HLA-DRB1*04:05 or *15:01	PCR	MS	Phenotypic risk	The rates of positive CSF findings and OCB positivity were significantly higher in HLA-DRB1*04:05-negative and HLA-DRB1*15:01-positive MS patients than in HLA-DRB1*04:05-positive and HLA-DRB1*15:01-negative patients.	N/A	25583844	Details
TRBV20OR9-2	Gene Polymorphism	BV8S3	PCR	MS	Disease risk	germ-line polymorphism in the TCRBV locus makes a major contribution to MS susceptibility	No significant differences in allele, genotype, or phenotype frequencies were observed between the MS patients and controls for any of the 19 TCRBV-gene polymorphisms studied	7717407	Details
CLEC16A	SNP	rs6498169	PCR	MS	Disease risk	Associations of CLEC16A polymorphisms with T1D and MS were successfully replicated in a Spanish population. A novel association of rs6498169 with a predisposition to RA was described which is consistent with previous MHC2TA results. These data provide evidence for the influence of variants within this chromosomal region on the development of complex diseases.	Genome-wide studies have identified the chromosomal region 16p13 in the susceptibility to type 1 diabetes (T1D) and multiple sclerosis (MS).	19221398	Details
HLA-DPB1	restriction fragment length polymorphism	N/A	PCR	MS	Disease risk	No polymorphism discriminating between MS and control pools was seen using DRB, DPa, DPB, TcRa, orTcRB geneprobes	The use of DNA pooled from groups of patients and controls from northeast Scotland enabled the screening of 14 restriction endonucleases with five HLA-D region probes (DPa, DPB, DQa, DQRB) and two T-cell antigen receptor probes	2567726	Details
IL4	allele	I3(2580) A	PCR	MS	Phenotype risk	Disease course analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
IRF8	SNP	rs17445836	PCR	MS	Disease risk	No SNP was associated with systematic deflection in time to disability milestones, age at onset or time to secondary progression.	N/A	22732448	Details
HLA-DRB1	polymorphisms	DRB1*13:01	PCR	MS	Disease risk	The following major histocompatibility complex risk alleles were replicated: HLADRB1*15:01, HLA-DRB1*03:01, as well as HLA-DRB1*04:05 and the African-specific risk allele of HLA-DRB1*15:03.	N/A	23771490	Details
TRBV20OR9-2	Gene Polymorphism	BV10S1	PCR	MS	Disease risk	germ-line polymorphism in the TCRBV locus makes a major contribution to MS susceptibility	No significant differences in allele, genotype, or phenotype frequencies were observed between the MS patients and controls for any of the 20 TCRBV-gene polymorphisms studied	7717407	Details
CLEC16A	SNP	rs6498169	PCR	MS	Disease risk	Associations of CLEC16A polymorphisms with T1D and MS were successfully replicated in a Spanish population. A novel association of rs6498169 with a predisposition to RA was described which is consistent with previous MHC2TA results. These data provide evidence for the influence of variants within this chromosomal region on the development of complex diseases.	Genome-wide studies have identified the chromosomal region 16p13 in the susceptibility to type 1 diabetes (T1D) and multiple sclerosis (MS).	19221398	Details
TRBV20OR9-2	restriction fragment length polymorphism	N/A	PCR	MS	Disease risk	No polymorphism discriminating between MS and control pools was seen using DRB, DPa, DPB, TcRa, orTcRB geneprobes	The use of DNA pooled from groups of patients and controls from northeast Scotland enabled the screening of 14 restriction endonucleases with five HLA-D region probes (DPa, DPB, DQa, DQRB) and two T-cell antigen receptor probes	2567726	Details
IL4	allele	I3(2580) C	PCR	MS	Phenotype risk	Disease course analysis in IL4	IL-4 inhibits the synthesis of IFNg	12667657	Details
CD226	SNP	rs763361	PCR	MS	Disease risk	No SNP was associated with systematic deflection in time to disability milestones, age at onset or time to secondary progression.	N/A	22732448	Details
HLA-DRB1	polymorphisms	DRB1*10:01	PCR	MS	Disease risk	The following major histocompatibility complex risk alleles were replicated: HLADRB1*15:01, HLA-DRB1*03:01, as well as HLA-DRB1*04:05 and the African-specific risk allele of HLA-DRB1*15:03.	N/A	23771490	Details
TRBV20OR9-2	Gene Polymorphism	BV12S2	PCR	MS	Disease risk	germ-line polymorphism in the TCRBV locus makes a major contribution to MS susceptibility	No significant differences in allele, genotype, or phenotype frequencies were observed between the MS patients and controls for any of the 21 TCRBV-gene polymorphisms studied	7717407	Details
TBATAp	SNP	rs2791196	PCR	MS	Disease risk	We found the association of rs2791196 with the MS group and RRMS patients	These findings suggest C10orf27 as a candidate gene for MS susceptibility and pathogenesis	18208870	Details
HLA-DRB1	Allele	NA	PCR	MS	Disease risk	The J genetic variability and are involved in the transport of mutation was not found in linkage disequilibrium with antigenic peptides from the cytoplasm to the endoplasmic the HLA-DRB lx 150 1 allele and can be considered an reticulum. Comparison of 116 MS patients with Cauca- additional genetic susceptibility marker of the disease.	MS is an autoimmune demyelinating dis- between the previously described alleles of the TAP1 and ease that has been known to be associated with the HLA- TAP2 genes and MS. We report here an additional TAP2 DRB1*1501-DQA1*0102-DQB1~0602 haplotype.	7759306	Details
HLA-DPB1	restriction fragment length polymorphism	N/A	PCR	MS	Disease risk	Using sequence-specific oligonucleotide probes, no altered distribution in the frequency of HLA-DPB1 alleles was found in multiple sclerosis patients from Northern Ireland. Although present in the controls, linkage disequilibrium between HLA-DPBl*OlOl and HLA-DR17 was not found in multiple sclerosis patients.	We have extended our previous study by oligonucleotide typing the same group of patients for HLA-DPB1 alleles and comparing the frequency of these alleles with controls from the same population.	1420118	Details
TGFB1	haplotype	GCTGC	PCR	MS	Disease risk	TGFB1 haplotype frequencies in the familial MS dataset	In conclusion, our findings suggest that TGFB1 or a nearby locus affects disease expression.	11311337	Details
TYK2	SNP	rs34536443	PCR	MS	Disease risk	No SNP was associated with systematic deflection in time to disability milestones, age at onset or time to secondary progression.	Tyk2 is a dendritic cell signalling protein which causes a shift towards the Th1 response in response to IL-12, which may be important in early inflammatory stages of MS.	22732448	Details
HLA-DRB1	polymorphisms	DRB1*13:02	PCR	MS	Disease risk	The following major histocompatibility complex risk alleles were replicated: HLADRB1*15:01, HLA-DRB1*03:01, as well as HLA-DRB1*04:05 and the African-specific risk allele of HLA-DRB1*15:03.	N/A	23771490	Details
MMP9	polymorphisms	MMP-9 -1562 C/T	PCR	MS	Disease risk	In the patients group overall, genotype and allele frequency distributions were not significantly different between patients and controls. We found a significant decrease in T allele carrier frequency in female patients with MS compared to healthy female controls, which remained significant after correction for multiple testing.	Matrix metalloproteinases (MMPs) are proteolytic enzymes involved in remodeling of the extracellular matrix.They are suggested to play a role in the influx of inflammatory cells into the CNS, disruption of the BBB, and have been shown to degrade myelin in vitro.Its production is instrumental in regulating the size-differentiated opening of the BBB during acute neuroinflammation.	17655938	Details
TRBV20OR9-2	Gene Polymorphism	BV15S1	PCR	MS	Disease risk	germ-line polymorphism in the TCRBV locus makes a major contribution to MS susceptibility	No significant differences in allele, genotype, or phenotype frequencies were observed between the MS patients and controls for any of the 22 TCRBV-gene polymorphisms studied	7717407	Details
TBATAp	SNP	rs2791196	PCR	MS	Disease risk	At rs2254174,both T and TT were associated with PPMS after comparisons with RRMS,and negative associations were found for PPMS patients carrying the TC genotype	These findings suggest C10orf27 as a candidate gene for MS susceptibility and pathogenesis	18208870	Details
HLA-DQB1	Allele	NA	PCR	MS	Disease risk	The J genetic variability and are involved in the transport of mutation was not found in linkage disequilibrium with antigenic peptides from the cytoplasm to the endoplasmic the HLA-DRB lx 150 1 allele and can be considered an reticulum. Comparison of 116 MS patients with Cauca- additional genetic susceptibility marker of the disease.	MS is an autoimmune demyelinating dis- between the previously described alleles of the TAP1 and ease that has been known to be associated with the HLA- TAP2 genes and MS. We report here an additional TAP2 DRB1*1501-DQA1*0102-DQB1~0602 haplotype.	7759306	Details
TGFB1	haplotype	GTCGC	PCR	MS	Disease risk	TGFB1 haplotype frequencies in the familial MS dataset	In conclusion, our findings suggest that TGFB1 or a nearby locus affects disease expression.	11311337	Details
HLA-DPB1	SNP	rs2394160	PCR	MS	Disease risk	we identified seven SNPs that were independently associated with MS conditional on the others.	N/A	21049023	Details
HLA-DRB1	polymorphisms	DRB1*12:01	PCR	MS	Disease risk	The following major histocompatibility complex risk alleles were replicated: HLADRB1*15:01, HLA-DRB1*03:01, as well as HLA-DRB1*04:05 and the African-specific risk allele of HLA-DRB1*15:03.	N/A	23771490	Details
TRBV20OR9-2	Gene Polymorphism	BV16S1	PCR	MS	Disease risk	germ-line polymorphism in the TCRBV locus makes a major contribution to MS susceptibility	No significant differences in allele, genotype, or phenotype frequencies were observed between the MS patients and controls for any of the 23 TCRBV-gene polymorphisms studied	7717407	Details
TBATAp	SNP	rs12221473	PCR	MS	Disease risk	A modest excess of CA heterozygocity at rs12221473 in male patients with RRMS supports the indications of gender differences in genetic susceptibility for MS	These findings suggest C10orf27 as a candidate gene for MS susceptibility and pathogenesis	18208870	Details
APOE	Allele	NA	PCR	MS	Phenotypic risk	These results suggest no effect of the APOE genotype on susceptibility to MS, but indicate an association of the APOE ?4 allele with a more severe course of the disease.	Apolipoprotein E (apoE) influences the high-affinity binding of low-density lipoproteins (LDL) to their receptor.	11552016	Details
HLA-DPB1	HLA-DP β	N/A	PCR	MS	N/A	In contrast to previous reports, no DP beta allele was found to be increased in either patient population.	N/A	2391251	Details
TGFB1	haplotype	GCCCC	PCR	MS	Disease risk	TGFB1 haplotype frequencies in the familial MS dataset	In conclusion, our findings suggest that TGFB1 or a nearby locus affects disease expression.	11311337	Details
HLA-DPB1	SNP	rs2854050	PCR	MS	Disease risk	we identified seven SNPs that were independently associated with MS conditional on the others.	N/A	21049023	Details
HLA-DRB1	polymorphisms	DRB1*01:01	PCR	MS	Disease risk	The following major histocompatibility complex risk alleles were replicated: HLADRB1*15:01, HLA-DRB1*03:01, as well as HLA-DRB1*04:05 and the African-specific risk allele of HLA-DRB1*15:03.	N/A	23771490	Details
CD226	SNP	rs763361	PCR	MS	Disease risk	The frequency of T allele and TT genotype were also not increased in MS patients compare to the controls.	CD226 belongs to the immunoglobulin supergene family of receptors and was widely expressed on the CD4+ and CD8+ T cells, natural killer cells, monocytes, b cells and platelets. CD226 could lead to various biological responses, including target cell lysis and immune cell activation.Rs763361/Gly307Ser in the immune response gene CD226 on chromosome 18q22 may increase the susceptibility of multiple autoimmune diseases, such as Type 1 diabetes (T1D), autoimmune thyroid disease (AITD) and rheumatoid arthritis (RA).	22728856	Details
TRBV20OR9-2	Gene Polymorphism	BV21S4	PCR	MS	Disease risk	germ-line polymorphism in the TCRBV locus makes a major contribution to MS susceptibility	No significant differences in allele, genotype, or phenotype frequencies were observed between the MS patients and controls for any of the 24 TCRBV-gene polymorphisms studied	7717407	Details
HIF1A	SNP	rs11549465	PCR	MS	Disease risk	our results do not show a significant association between MS and HIF-1α polymorphisms	Some lines of evidence, suchas an increased protein level of HIF-1α, increased expression ofhypoxia-inducible genes in lesions and a reduction in blood flow inthe adjacent normal-appearing white matter of the lesion, supportthe role of hypoxia in early MS	31652374	Details
MBP	Allele	NA	PCR	MS	Disease risk	W e concluded that the MBP gene does not play a role in MS susceptibility in Sardini-ans.	A link between myelin basic protein (MBP) polymor-phism and multiple sclerosis (MS)has been reported in some popula-tions but not in others	12420096	Details
TGFB1	haplotype	ACTGC	PCR	MS	Disease risk	TGFB1 haplotype frequencies in the familial MS dataset	In conclusion, our findings suggest that TGFB1 or a nearby locus affects disease expression.	11311337	Details
HLA-DPB1	SNP	rs3830041	PCR	MS	Disease risk	we identified seven SNPs that were independently associated with MS conditional on the others.	N/A	21049023	Details
HLA-DQB1	polymorphisms	DQB1*02e	PCR	MS	Disease risk	None of the HLA-DQB1 alleles were associated with MS.	N/A	23771490	Details
TRBV20OR9-2	Gene Polymorphism	BV24S1	PCR	MS	Disease risk	germ-line polymorphism in the TCRBV locus makes a major contribution to MS susceptibility	No significant differences in allele, genotype, or phenotype frequencies were observed between the MS patients and controls for any of the 25 TCRBV-gene polymorphisms studied	7717407	Details
VEGFA	SNP	rs699947	PCR	MS	Disease risk	we showed a significant relationship between the VEGF rs699947 polymorphism and MS in a dominant inheritance model	VEGF has a major role in neurodegenerative diseases via inflammation	31652374	Details
TGFB1	Allele	NA	PCR	MS	Disease risk	In summary, we suggest that in males, a higher TGF-β1 level determined by TGFB1T[-509]T genotype in combination with the TGFBR2G[-875]A genotype might be a protective factor against RRMS development.	Multiple sclerosis (MS) is a chronic progressive autoimmune disease characterised by nerve demye-lination, mediated by myelin-specific Th1 autoreactive cells.	33480235	Details
TGFB1	haplotype	GCCGC	PCR	MS	Disease risk	TGFB1 haplotype frequencies in the familial MS dataset	In conclusion, our findings suggest that TGFB1 or a nearby locus affects disease expression.	11311337	Details
HLA-DPB1	SNP	rs3129939	PCR	MS	Disease risk	we identified seven SNPs that were independently associated with MS conditional on the others.	N/A	21049023	Details
HLA-DQB1	polymorphisms	DQB1*03:01	PCR	MS	Disease risk	None of the HLA-DQB1 alleles were associated with MS.	N/A	23771490	Details
TRBV20OR9-2	Gene Polymorphism	BV25S1	PCR	MS	Disease risk	germ-line polymorphism in the TCRBV locus makes a major contribution to MS susceptibility	No significant differences in allele, genotype, or phenotype frequencies were observed between the MS patients and controls for any of the 26 TCRBV-gene polymorphisms studied	7717407	Details
HLA-DRB1	SNP	DRB1*1501	PCR	MS	Disease risk	The frequency of HLA-DRB1 * 1501 allele in the Western-type MS group increased significantly compared with the control group, while Asian-type MS and control groups showed similar distribution in the frequencies of HLA-DRB1 alleles	The results suggest that MS in Asians may present two different clinical and immunogenetic manifestations	9916885	Details
TGFBR2	Allele	NA	PCR	MS	Disease risk	In summary, we suggest that in males, a higher TGF-β1 level determined by TGFB1T[-509]T genotype in combination with the TGFBR2G[-875]A genotype might be a protective factor against RRMS development.	Multiple sclerosis (MS) is a chronic progressive autoimmune disease characterised by nerve demye-lination, mediated by myelin-specific Th1 autoreactive cells.	33480235	Details
C3	SNP	rs2230199	PCR	MS	Disease risk	C3-rs2230199 affects white and GM damage as well as cognitive impairment in MS patients.	N/A	29485352	Details
TGFB1	haplotype	GTTGC	PCR	MS	Disease risk	TGFB1 haplotype frequencies in the familial MS dataset	In conclusion, our findings suggest that TGFB1 or a nearby locus affects disease expression.	11311337	Details
HLA-DPB1	SNP	rs9271366	PCR	MS	Disease risk	we identified seven SNPs that were independently associated with MS conditional on the others.	N/A	21049023	Details
HLA-DQB1	polymorphisms	DQB1*03:02	PCR	MS	Disease risk	None of the HLA-DQB1 alleles were associated with MS.	N/A	23771490	Details
TRBV20OR9-2	Gene Polymorphism	BV26S1	PCR	MS	Disease risk	germ-line polymorphism in the TCRBV locus makes a major contribution to MS susceptibility	No significant differences in allele, genotype, or phenotype frequencies were observed between the MS patients and controls for any of the 27 TCRBV-gene polymorphisms studied	7717407	Details
IRF5	SNP	rs2004640	PCR	MS	Treatment risk	Genetic analysis of the studied gene variants do not provide additional information.	Single nucleotide polymorphisms (SNPs) in the genes encoding interferon response factor (IRF)-5, IRF-8 and glypican-5 (GPC5) have been associated with disease activity in multiple sclerosis (MS) patients treated with interferon (IFN)-b.	24943672	Details
MIR155	SNP	rs767649	PCR	MS	N/A	These results showed that individuals carrying the genotypes of rs3745453 TC had a 2.3-fold increased risk of MS (OR=2.3, p=0.048). There was no significant difference between genotypes and allele frequency of mir155 and mir196a2 in patients and healthy controls.	N/A	30518189	Details
TGFB1	haplotype	GTCGT	PCR	MS	Disease risk	TGFB1 haplotype frequencies in the familial MS dataset	In conclusion, our findings suggest that TGFB1 or a nearby locus affects disease expression.	11311337	Details
HLA-DPB1	SNP	rs2187668	PCR	MS	Disease risk	we identified seven SNPs that were independently associated with MS conditional on the others.	N/A	21049023	Details
HLA-DQB1	polymorphisms	DQB1*03:03	PCR	MS	Disease risk	None of the HLA-DQB1 alleles were associated with MS.	N/A	23771490	Details
Ncf1	allele	amino acid replacements at position 106 and 153	PCR	EAE	Phenotypic risk	MOG79–96 peptide-induced EAE was milder in the Ncf1-mutated mice than in the wild-type control.However, induction of EAE with MOG protein induced a more severe chronic EAE in the Ncf1-mutated mice.	Ncf1 has a more general role in regulating autoimmune inflammation and also suggests that the effect of Ncf1 is related to the function of antigen-presenting cells (APC) in processing and presenting autoantigens to T cells.	15310853	Details
NPY	SNP	rs16139	PCR	MS	Disease risk	In conclusion, obtained results demonstrate the probable role of NPY SNPs in susceptibility to MS within the Iranian population.	the maintenance of homeostasis in the immune system and coping of stress condition	27559040	Details
IRF5	SNP	rs3807306	PCR	MS	Treatment risk	Genetic analysis of the studied gene variants do not provide additional information.	Single nucleotide polymorphisms (SNPs) in the genes encoding interferon response factor (IRF)-5, IRF-8 and glypican-5 (GPC5) have been associated with disease activity in multiple sclerosis (MS) patients treated with interferon (IFN)-b.	24943672	Details
MIR196A2	SNP	rs11614913	PCR	MS	N/A	These results showed that individuals carrying the genotypes of rs3745453 TC had a 2.3-fold increased risk of MS (OR=2.3, p=0.048). There was no significant difference between genotypes and allele frequency of mir155 and mir196a2 in patients and healthy controls.	N/A	30518189	Details
HLA-A	genotype	A1	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
TGFB1	haplotype	Rare C	PCR	MS	Disease risk	TGFB1 haplotype frequencies in the familial MS dataset	In conclusion, our findings suggest that TGFB1 or a nearby locus affects disease expression.	11311337	Details
HLA-DPB1	SNP	rs9277535	PCR	MS	Disease risk	we identified seven SNPs that were independently associated with MS conditional on the others.	N/A	21049023	Details
HLA-DQB1	polymorphisms	DQB1*04:02	PCR	MS	Disease risk	None of the HLA-DQB1 alleles were associated with MS.	N/A	23771490	Details
NPY	SNP	rs16147	PCR	MS	Disease risk	In conclusion, obtained results demonstrate the probable role of NPY SNPs in susceptibility to MS within the Iranian population.	the maintenance of homeostasis in the immune system and coping of stress condition	27559040	Details
IRF5	SNP	rs4728142	PCR	MS	Treatment risk	Genetic analysis of the studied gene variants do not provide additional information.	Single nucleotide polymorphisms (SNPs) in the genes encoding interferon response factor (IRF)-5, IRF-8 and glypican-5 (GPC5) have been associated with disease activity in multiple sclerosis (MS) patients treated with interferon (IFN)-b.	24943672	Details
HLA-A	genotype	A2	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DRB1	polymorphism	DRB1*15	PCR	MS	Disease risk	The specificity of the DRB1*15 risk allele for children with subsequent MS diagnosis, but not for all children with ADS.	N/A	21288988	Details
HLA-DQB1	polymorphisms	DQB1*05:01	PCR	MS	Disease risk	None of the HLA-DQB1 alleles were associated with MS.	N/A	23771490	Details
IFNAR1	SNP	rs2850015	PCR	MS	Treatment risk	rs2850015 SNP indicated a statistically signifcant diference between the responders and non-responders.There was a signifcant diference between the responders and non-responders concerning the TC genotype.The results implied that compared to the CC genotype, the probability of response to treatment was higher in the TC genotype.	IFN-β binds to type I interferon receptors and persuades a complex transcriptional response, allowing multiple immunomodulatory proteins expression. Thus, up-or down-regulation of the IFNAR1 and IFNAR2 receptors could afect the IFN-β therapy.	34328599	Details
IRF8	SNP	rs13333054	PCR	MS	Treatment risk	Genetic analysis of the studied gene variants do not provide additional information.	Single nucleotide polymorphisms (SNPs) in the genes encoding interferon response factor (IRF)-5, IRF-8 and glypican-5 (GPC5) have been associated with disease activity in multiple sclerosis (MS) patients treated with interferon (IFN)-b.	24943672	Details
IL7R	SNP	rs6897932	PCR	MS	Disease risk	Higher significant frequencies of the T allele and TT genotype for rs6897932 (C/T) were observed in patients comparing to controls (p=0.006). Higher frequencies of the T allele and the TT and TG genotypes and lower frequencies of the G allele and GG genotypes for rs201084372 (G/A) were found in patients comparing to controls (p<0.0001)	N/A	28865414	Details
HLA-A	genotype	A11	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
Tcrb	rearrangement	Vβ8.2	PCR	EAE	Disease risk	Vaccination with Vb8.2 DNA protects from EAE.	N/A	8705860	Details
IFNG	marker	D12S1676	PCR	MS	Disease risk	Only D12S375 was weakly associated with MS in the ‘low HLA-risk’ group (ie individuals carrying neither DRB1*03 nor DRB1*04 alleles) (P 0.024), especially in men (P 0.049).	N/A	12486605	Details
CTLA4	polymorphism	position 318 of the CTLA4 promoter	PCR	MS	Disease risk	however, there was a clear relationship between genotype and CTLA-4 expression.	N/A	11426323	Details
HLA-DQB1	polymorphisms	DQB1*05:02	PCR	MS	Disease risk	None of the HLA-DQB1 alleles were associated with MS.	N/A	23771490	Details
IRF8	SNP	rs17445836	PCR	MS	Treatment risk	Genetic analysis of the studied gene variants do not provide additional information.	Single nucleotide polymorphisms (SNPs) in the genes encoding interferon response factor (IRF)-5, IRF-8 and glypican-5 (GPC5) have been associated with disease activity in multiple sclerosis (MS) patients treated with interferon (IFN)-b.	24943672	Details
IL7R	SNP	rs201084372	PCR	MS	Disease risk	Higher significant frequencies of the T allele and TT genotype for rs6897932 (C/T) were observed in patients comparing to controls (p=0.006). Higher frequencies of the T allele and the TT and TG genotypes and lower frequencies of the G allele and GG genotypes for rs201084372 (G/A) were found in patients comparing to controls (p<0.0001)	N/A	28865414	Details
HLA-A	genotype	A24	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
IFNG	marker	D12S375	PCR	MS	Disease risk	Only D12S375 was weakly associated with MS in the ‘low HLA-risk’ group (ie individuals carrying neither DRB1*03 nor DRB1*04 alleles) (P 0.024), especially in men (P 0.049).	N/A	12486605	Details
CTLA4	polymorphism	position 49 in exon 1	PCR	MS	Disease risk	however, there was a clear relationship between genotype and CTLA-4 expression.	N/A	11426323	Details
HLA-DQB1	polymorphisms	DQB1*05:03	PCR	MS	Disease risk	None of the HLA-DQB1 alleles were associated with MS.	N/A	23771490	Details
APOE	Gene polymorphisms	ε4	PCR	MS	Disease risk	During follow-up, the drop in the N-acetylaspartate-creatine ratio of epsilon4 carriers was also significantly larger (-0.31 vs -0.10; P =.01)	The APOE epsilon4 allele has a negative effect on the course of MS, and increasing axonal damage may be an important mechanism	12533090	Details
GPC5	SNP	rs10492503	PCR	MS	Treatment risk	Genetic analysis of the studied gene variants do not provide additional information.	Single nucleotide polymorphisms (SNPs) in the genes encoding interferon response factor (IRF)-5, IRF-8 and glypican-5 (GPC5) have been associated with disease activity in multiple sclerosis (MS) patients treated with interferon (IFN)-b.	24943672	Details
HLA-A	genotype	A26	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DRB1	SNP	rs3135388	PCR	MS	Disease risk	Our results indicate that the distribution of the rs3135388 gene polymorphism is a risk factor for MS susceptibility in the Czech female population.	N/A	23186557	Details
IFNG	marker	D12S1680	PCR	MS	Disease risk	Only D12S375 was weakly associated with MS in the ‘low HLA-risk’ group (ie individuals carrying neither DRB1*03 nor DRB1*04 alleles) (P 0.024), especially in men (P 0.049).	N/A	12486605	Details
HLA-DQB1	polymorphisms	DQB1*06:02	PCR	MS	Disease risk	None of the HLA-DQB1 alleles were associated with MS.	N/A	23771490	Details
HLA-A	genotype	A39	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
MT-TT	variation	G15257A	PCR	MS	Disease risk	The mtDNA G15257A variation was found in one of the 100 patients and one of the 100 controls.	Mitochondrial DNA (mtDNA) is more vulnerable to damage and mutation than nuclear DNA, due to the highly oxidizing environment of the mitochondria.	26233806	Details
IFNG	marker	D12S1052	PCR	MS	Disease risk	Only D12S375 was weakly associated with MS in the ‘low HLA-risk’ group (ie individuals carrying neither DRB1*03 nor DRB1*04 alleles) (P 0.024), especially in men (P 0.049).	N/A	12486605	Details
HLA-DQB1	polymorphisms	DQB1*06:03	PCR	MS	Disease risk	None of the HLA-DQB1 alleles were associated with MS.	N/A	23771490	Details
CNR1	allele	short AAT , long AAT	PCR	MS	Phenotypic risk	The two genotype groups (short and long AAT) did not differ in terms of the main clinical and demographic characteristics.	Genetic ablation of CB1Rs exacerbates the neurodegenerative damage associated with experimental autoimmune encephalomyelitis (EAE), a reliable mouse model of multiple sclerosis (MS), by altering synaptic sensitivity to pro-inflammatory cytokines released by infiltrating immune cells and by activated microglia. Inflammation leads to neuronal damage also in the human brain, and indeed higher frequency and severity of inflammatory episodes have been associated with accelerated neurodegeneration and disability accumulation in MS.	24391723	Details
ACE	ACE homozygotes, II	N/A	PCR	MS	Disease risk	Both ACE homozygotes, II and DD, were significantly overrepresented in MS patients, compared to controls (χ(2) test p=0.03).	N/A	27000216	Details
HLA-A	genotype	A31	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
MT-TT	variation	G15812A	PCR	MS	Disease risk	The mtDNA G15812A variation was not found in any of the 100 patients or 100 controls.	Mitochondrial DNA (mtDNA) is more vulnerable to damage and mutation than nuclear DNA, due to the highly oxidizing environment of the mitochondria.	26233806	Details
TGFB1	genotype	+869 TT	PCR	MS	Disease risk	However, the TGFB11869 genotype CC was significantly more frequent in patients (p 5 0.031, x2 test).	N/A	15450129	Details
HLA-DQB1	polymorphisms	DQB1*06:04	PCR	MS	Disease risk	None of the HLA-DQB1 alleles were associated with MS.	N/A	23771490	Details
ACE	ACE homozygotes,DD	N/A	PCR	MS	Disease risk	Both ACE homozygotes, II and DD, were significantly overrepresented in MS patients, compared to controls (χ(2) test p=0.03).	N/A	27000216	Details
HLA-A	genotype	Aw33	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
TGFB1	genotype	+869 TC	PCR	MS	Disease risk	However, the TGFB11869 genotype CC was significantly more frequent in patients (p 5 0.031, x2 test).	N/A	15450129	Details
Fas	mutation	Fas+/-	PCR	EAE	Disease risk	The differences between Fas-/- group and the other two groups are statistically significant.	N/A	10866127	Details
HLA-DQB1	polymorphisms	DQB1*06:09	PCR	MS	Disease risk	None of the HLA-DQB1 alleles were associated with MS.	N/A	23771490	Details
ACE	AT1R 1166A/C	N/A	PCR	MS	N/A	Neither genotype nor allele frequencies of AT1R 1166A/C polymorphism were significantly different between patients and controls.	N/A	27000216	Details
HLA-B	genotype	B7	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
TGFB1	genotype	+869 CC	PCR	MS	Disease risk	However, the TGFB11869 genotype CC was significantly more frequent in patients (p 5 0.031, x2 test).	N/A	15450129	Details
Fas	mutation	Fas-/-	PCR	EAE	Disease risk	The differences between Fas-/- group and the other two groups are statistically significant.	N/A	10866127	Details
IL7R	SNP	rs6897932	PCR	MS	Disease risk	Moreover, we revealed for the first time that rs6897932 in IL7Ra gene is associated with the progression of MS, evaluated by MSSS scores.	N/A	25903732	Details
HLA-B	genotype	B13	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
TGFB1	allel	+869 C	PCR	MS	Disease risk	The highest frequency of the TGFB11869 genotype CC was observed in male patients (25.2% vs. 10.0% in controls, p 5 0.004, x2 test), and carriership of TGFB11869 allele C was correspondingly increased in male patients	N/A	15450129	Details
FasL	mutation	FasL+/-	PCR	EAE	Disease risk	The difference between FasL-/- and FasL-/+ group is only statistically significant for male mice.	N/A	10866127	Details
CIITA	SNP	rs4774 * C	PCR	MS	Disease risk	Furthermore, we observed that the +1614G/C mutation in combination with the HLA-DRB1*15:01 allele increased susceptibility to MS in females (OR = 4.55; p = 0.01).	N/A	25992516	Details
HLA-B	genotype	B14	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
TGFB1	allel	+869 T	PCR	MS	Disease risk	The highest frequency of the TGFB11869 genotype CC was observed in male patients (25.2% vs. 10.0% in controls, p 5 0.004, x2 test), and carriership of TGFB11869 allele C was correspondingly increased in male patients	N/A	15450129	Details
FasL	mutation	FasL-/-	PCR	EAE	Disease risk	The difference between FasL-/- and FasL-/+ group is only statistically significant for male mice.	N/A	10866127	Details
HLA-DRB1	HLA-DRB1*15:01	N/A	PCR	MS	Disease risk	Furthermore, we observed that the +1614G/C mutation in combination with the HLA-DRB1*15:01 allele increased susceptibility to MS in females (OR = 4.55; p = 0.01).	N/A	25992516	Details
HLA-B	genotype	B17	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DQB1	haplotype	DRB5*0101-DQA1*0102-DQB1*0602	PCR	MS	Disease risk	By the RPE method, the DR2 haplotype, DRB5*0101-DQA1*0102 DQB1*0602, was found to be predispositional (Z = 3.54; p < 0.0004) and had a RR = 2.43; 95% confidence interval (CI) for the RR was 1.43 to 4.13.	N/A	8780100	Details
TGFB1	genotype	+915 GG	PCR	MS	Disease risk	N/A	N/A	15450129	Details
TNF	Gene polymorphisms	TNF - 238	PCR	MS	Disease risk	These results suggest that the -238 GG genotype is differently distributed in hospitalized MS patients in a nursing home;The -238 G to A polymorphism is differently distributed in hospitalized MS patients in a nursing home compared to healthy controls	TNF-α promoter polymorphisms and susceptibility to MS	9042107	Details
HLA-B	genotype	B27	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DQA1	haplotype	DRB5*0101-DQA1*0102-DQB1*0602	PCR	MS	Disease risk	By the RPE method, the DR2 haplotype, DRB5*0101-DQA1*0102 DQB1*0602, was found to be predispositional (Z = 3.54; p < 0.0004) and had a RR = 2.43; 95% confidence interval (CI) for the RR was 1.43 to 4.13.	N/A	8780100	Details
TGFB1	genotype	+915 GC	PCR	MS	Disease risk	N/A	N/A	15450129	Details
CD40	SNP	rs4810485*T	PCR	MS	Disease risk	We found that carrying the risk allele rs4810485*T lowered the cell-surface expression of CD40 in all tested B cell subtypes, while carrying the risk allele rs9282641*G increased the expression of CD86.	N/A	29361022	Details
NCF1	Deletion	dinucleotide deletion (ΔGT) in exon 2	PCR	MS	Disease risk	DeltaGT/GTGT ratios were not associated with susceptibility to MS.	The ΔGT/GTGT ratio influences the expression levels of NCF1 most probably by the occurrence of an NCF1 transcript from the type II pseudogene that does not contain the GT deletion, which leads to a premature stop codon in the type I pseudogene.	19077231	Details
HLA-B	Allele	NA	PCR	MS	Disease risk	Neither HLA-B nor HLA-DR alleles were found to be associated with MS susceptibility.	It is well known that certain HLA class II alleles confer an increased risk for developing multiple sclerosis (MS). Recent studies have suggested HLA class I as a region that may also contribute to the development of MS.	16671949	Details
HLA-B	genotype	B35	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DRB5	haplotype	DRB5*0101-DQA1*0102-DQB1*0602	PCR	MS	Disease risk	By the RPE method, the DR2 haplotype, DRB5*0101-DQA1*0102 DQB1*0602, was found to be predispositional (Z = 3.54; p < 0.0004) and had a RR = 2.43; 95% confidence interval (CI) for the RR was 1.43 to 4.13.	N/A	8780100	Details
TGFB1	genotype	+915 CC	PCR	MS	Disease risk	N/A	N/A	15450129	Details
CD86	SNP	rs9282641*G	PCR	MS	Disease risk	We found that carrying the risk allele rs4810485*T lowered the cell-surface expression of CD40 in all tested B cell subtypes, while carrying the risk allele rs9282641*G increased the expression of CD86.	N/A	29361022	Details
NCF1	Deletion	dinucleotide deletion (ΔGT) in exon 2	PCR	MS	Disease risk	DeltaGT/GTGT ratios were not associated with susceptibility to MS.	The ΔGT/GTGT ratio influences the expression levels of NCF1 most probably by the occurrence of an NCF1 transcript from the type II pseudogene that does not contain the GT deletion, which leads to a premature stop codon in the type I pseudogene.	19077231	Details
HLA-DRB1	Allele	NA	PCR	MS	Disease risk	Neither HLA-B nor HLA-DR alleles were found to be associated with MS susceptibility.	It is well known that certain HLA class II alleles confer an increased risk for developing multiple sclerosis (MS). Recent studies have suggested HLA class I as a region that may also contribute to the development of MS.	16671949	Details
HLA-B	genotype	B37	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DRB1	haplotype	DRB1*1302-DQA1*0102-DQBl*0604	PCR	MS	Disease risk	After removal of this DR2 haplotype from the analysis, a DR13 haplotype (DRB1'~1302-DQA1'''0102-DQBl"0604) was found to be protective (Z = 2.04; p < 0.04) and had a RR = 0.33; 95% CI for the RR was 0.13 to 0.82.	N/A	8780100	Details
TGFB1	allel	+915 G	PCR	MS	Disease risk	N/A	N/A	15450129	Details
CD40	SNP	rs4810485*T	PCR	MS	Disease risk	Finally, we also observed that the risk allele rs4810485*T was associated with decreased levels of interleukin-10 (P = 0.020).	It is considered to have an immunoregulatory function downstream of CD40.	29361022	Details
HLA-B	genotype	B38	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DQB1	haplotype	DRB1*1302-DQA1*0102-DQBl*0604	PCR	MS	Disease risk	After removal of this DR2 haplotype from the analysis, a DR13 haplotype (DRB1'~1302-DQA1'''0102-DQBl"0604) was found to be protective (Z = 2.04; p < 0.04) and had a RR = 0.33; 95% CI for the RR was 0.13 to 0.82.	N/A	8780100	Details
TGFB1	allel	+915 C	PCR	MS	Disease risk	N/A	N/A	15450129	Details
GAL	allele	rs948854(G)	PCR	MS	Disease risk	The minor allele (G) increased susceptibility to MS in men.	Although it remains to be determined whether A-to-G substitution in rs948854 reduces GAL transcription, a subsequent reduction in the galanin level, if confirmed, likely contributes to the increased susceptibility to MS, whereas testosterone may temporarily protect male carriers from MS onset.	27870457	Details
HLA-DMB	Allele	NA	PCR	MS	Disease risk	Patients with predominant responses to different MBP epitopes did not differ for their HLA-DM haplotype while patients with predominant responses to the same MBP epitope could present different HLA-DM haplotypes. HLA-DM polymorphisms do not associate with MS and may not affect specific patterns of T cell responses to MBP	The MHC region on 6p harbors at least one susceptibility gene for multiple sclerosis MS . Within this region, HLA-DM loci are of interest being involved in class II antigen processing.	9258248	Details
HLA-B	genotype	B39	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DQA1	haplotype	DRB1*1302-DQA1*0102-DQBl*0604	PCR	MS	Disease risk	After removal of this DR2 haplotype from the analysis, a DR13 haplotype (DRB1'~1302-DQA1'''0102-DQBl"0604) was found to be protective (Z = 2.04; p < 0.04) and had a RR = 0.33; 95% CI for the RR was 0.13 to 0.82.	N/A	8780100	Details
GAL	allele	rs948854(G)	PCR	MS	Phenotypic risk	The G allele in men was also significantly associated with the late onset of MS.	N/A	27870457	Details
MMP9	polymorphism	1562 C/T	PCR	MS	Disease risk	In the patients group overall, genotype and allele frequency distributions were not significantly different between patients and controls. We found a significant decrease in T allele carrier frequency in female patients with MS compared to healthy female controls.	Matrix metalloproteinases (MMPs) are proteolytic enzymes involved in remodeling of the extracellular matrix. They are suggested to play a role in the influx of inflammatory cells into the CNS, disruption of the BBB, and have been shown to degrade myelin in vitro .	17655938	Details
IFNG	gene Polymorphism	N/A	PCR	MS	Disease risk	I2 is significantly more often transmitted to DRB1*032/*042 males, than to DRB1*032/*042 females. The odds ratio (OR) for IFNG-associated susceptibility to MS in the total Sardinian DRB1*032/*042 group was 1.88 for I2 heterozygotes but amounted to 8.235 for I2 homozygotes, suggestive of a recessive mode of inheritance	a recessive mode of inheritance	10505747	Details
HLA-DMA	Allele	NA	PCR	MS	Disease risk	Patients with predominant responses to different MBP epitopes did not differ for their HLA-DM haplotype while patients with predominant responses to the same MBP epitope could present different HLA-DM haplotypes. HLA-DM polymorphisms do not associate with MS and may not affect specific patterns of T cell responses to MBP	The MHC region on 6p harbors at least one susceptibility gene for multiple sclerosis MS . Within this region, HLA-DM loci are of interest being involved in class II antigen processing.	9258248	Details
HLA-B	genotype	B44	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DQB1	polymorphisms	DQBl"0201	PCR	MS	Disease risk	but not DQBl"0201 was protective.	N/A	8780100	Details
GAL	SNP	rs948854	PCR	MS	Phenotypic risk	Furthermore, rs948854 polymorphism affected the rate of MS progression depending on the sex of the patients.	N/A	27870457	Details
MMP9	polymorphism	1562 C/T	PCR	MS	Phenotypic risk	We did not find significant association of genotypes with disease severity expressed by MSSS.	Matrix metalloproteinases (MMPs) are proteolytic enzymes involved in remodeling of the extracellular matrix. They are suggested to play a role in the influx of inflammatory cells into the CNS, disruption of the BBB, and have been shown to degrade myelin in vitro .	17655938	Details
HLA-DRB1	gene Polymorphism	N/A	PCR	MS	Disease risk	I2 is significantly more often transmitted to DRB1*032/*042 males, than to DRB1*032/*042 females. The odds ratio (OR) for IFNG-associated susceptibility to MS in the total Sardinian DRB1*032/*042 group was 1.88 for I2 heterozygotes but amounted to 8.235 for I3 homozygotes, suggestive of a recessive mode of inheritance	a recessive mode of inheritance	10505747	Details
IL2	Allele	NA	PCR	MS	Disease risk	These data indicate for the first time the relevance of the il-2 gene locus in human MS and its possible involvement in other autoimmune diseases	We have investigated the association of two single nucleotide polymorphisms SNPs at positions y384 and 114 in the human interleukin-2 hIL-2 with multiple sclerosis MS . For two of the y384 genotypes GrT, TrT , we observed an association with the susceptibility to secondary progressive SP course of MS Ps0.005 and Ps0.013, respectively	11525806	Details
HLA-DRB1	HLA-DRB1 * 04 / * 07	N/A	PCR	MS	Disease risk	Incorporating these results in an analysis of MS risk, we identified a strong protective effect of HLA-DRB1*04, *07, and *09 (DR53) alleles (p = 10(-12)) and elevated risk associated with DRB1*15 and *16 (DR51) and *08 (DR8) alleles (p < 10(-18)).	An independent contribution of VDRE motif variation to increase MS risk was not discernible, although vitamin D-dependent regulation of HLA-DR expression may still play an important role given that HLA-DRB1*04/*07/*09 (DR53) alleles that express the "nonresponsive" VDRE motif were associated with significantly reduced risk of MS.	22786591	Details
HLA-B	genotype	Bw46	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DRB5	polymorphisms	DRB5*0101	PCR	MS	Disease risk	The significant difference obtained with the x2 disequilibrium statisticz3 (x2 = 6.55, p < 0.05) suggests that the DR2 allele and MS cosegregate and that there is linkage.	N/A	8780100	Details
APOE	Allele	NA	PCR	MS	Disease risk	Furthermore, we show that no particular apo E allele was associated with familial or sporadic MS. These results are different from those reported for AD.	Three common variants of apo E are present in the general human population, c2, d and Fa coding for three isoforms (apo E2, apo E3, apo E4). These isoforms differ from each other by a single aminoacid substitution. The most frequent phenotype in the normal population is apo E3/apo E3 and the two minor isoforms are associated with altered recognition of specific receptors.Recent genetic evidence suggests that inheritance of the c4 allele is associated with increased risk for sporadic and earlier onset of Alzheimer's disease (AD).2 In contrast, Rubinsztein found no influence of the apo E phenotype in a small group of patients with multiple sclerosis (MS)	9463752	Details
HLA-DRB1	HLA-DRB1*09 (DR53)	N/A	PCR	MS	Disease risk	Incorporating these results in an analysis of MS risk, we identified a strong protective effect of HLA-DRB1*04, *07, and *09 (DR53) alleles (p = 10(-12)) and elevated risk associated with DRB1*15 and *16 (DR51) and *08 (DR8) alleles (p < 10(-18)).	An independent contribution of VDRE motif variation to increase MS risk was not discernible, although vitamin D-dependent regulation of HLA-DR expression may still play an important role given that HLA-DRB1*04/*07/*09 (DR53) alleles that express the "nonresponsive" VDRE motif were associated with significantly reduced risk of MS.	22786591	Details
HLA-B	genotype	Bw48	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
PRNP	SNP	NA	PCR	MS	Disease risk	No deviations from Hardy-Weinberg equilibrium were observed for genotypes in the patient, parent, or com-bined group (data not shown).	Interestingly, it was also recently shown that the same Prnp129 SNP has a significant effect on the clinical course of nu-merous nonprion neurodegenerative disorders of the cen-tral nervous system (CNS), including early-onset Alz-heimer disease,2-4 Down syndrome,5 and Wilson disease.6 In these studies, methionine/valine (M/V) heterozygos-ity was associated with less severe clinical disease. Fi-nally, the Prnp129 SNP was also shown to negatively affect long-term memory in adult and senescent healthy indi-viduals.7-9 The exact mechanisms by which genetic poly-morphisms of Prnp alter CNS function and disease phe-notypes are largely unknown.	19204171	Details
HLA-DRB1	DRB1*15	N/A	PCR	MS	Disease risk	Incorporating these results in an analysis of MS risk, we identified a strong protective effect of HLA-DRB1*04, *07, and *09 (DR53) alleles (p = 10(-12)) and elevated risk associated with DRB1*15 and *16 (DR51) and *08 (DR8) alleles (p < 10(-18)).	An independent contribution of VDRE motif variation to increase MS risk was not discernible, although vitamin D-dependent regulation of HLA-DR expression may still play an important role given that HLA-DRB1*04/*07/*09 (DR53) alleles that express the "nonresponsive" VDRE motif were associated with significantly reduced risk of MS.	22786591	Details
HLA-B	genotype	B51	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
TNF	Allele	NA	PCR	MS	Phenotypic risk	Considering the association of different TNF-~ alleles with diverse autoimmune diseases we sequenced the TNF-u promotor region (-674 to +201) of 23 patients with relapsing/remitting MS, of 27 patients with chronic progressive MS (21 patients had primary progressive course and six patients had a secondary progressive course) and of 22 healthy controls, who had no history of MS in their families. In three of 21 patients (14%) with primary chronic progressive MS a homozygous point-mutation at position -308 could be demonstrated where guanine (G) was substituted by adenosine (A). This mutation could neither be detected in patients with relapsing/ remitting MS nor in healthy controls. However, 40% of the patients with relapsing/remitting MS and 43% of the primary chronic progressive MS patients were heterozygous at position -308 for G/A, whereas only 32% of healthy controls showed this heterogeneity.	Tumor-necrosis-factor-~ (TNF-c0 is a major mediator of the inflammatory immune response and may play an important role in the pathogenesis and progression of Multiple Sclerosis (MS).	8887999	Details
HLA-DRB1	*16 (DR51)	N/A	PCR	MS	Disease risk	Incorporating these results in an analysis of MS risk, we identified a strong protective effect of HLA-DRB1*04, *07, and *09 (DR53) alleles (p = 10(-12)) and elevated risk associated with DRB1*15 and *16 (DR51) and *08 (DR8) alleles (p < 10(-18)).	An independent contribution of VDRE motif variation to increase MS risk was not discernible, although vitamin D-dependent regulation of HLA-DR expression may still play an important role given that HLA-DRB1*04/*07/*09 (DR53) alleles that express the "nonresponsive" VDRE motif were associated with significantly reduced risk of MS.	22786591	Details
HLA-B	genotype	B52	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DRB1	*08 (DR8)	N/A	PCR	MS	Disease risk	Incorporating these results in an analysis of MS risk, we identified a strong protective effect of HLA-DRB1*04, *07, and *09 (DR53) alleles (p = 10(-12)) and elevated risk associated with DRB1*15 and *16 (DR51) and *08 (DR8) alleles (p < 10(-18)).	An independent contribution of VDRE motif variation to increase MS risk was not discernible, although vitamin D-dependent regulation of HLA-DR expression may still play an important role given that HLA-DRB1*04/*07/*09 (DR53) alleles that express the "nonresponsive" VDRE motif were associated with significantly reduced risk of MS.	22786591	Details
HLA-B	genotype	B54	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
IGH	N/A	IGHV1	PCR	MS	Disease risk	We find that all MOGspecific IgGκ Fab fragments, unrelated to genetic make-up, utilize a restricted set of variable region genes, IGHV1 and IGHV3 for the H chain and IGKV1, IGKV3, and IGKV5 for the L chain.	N/A	16528499	Details
STAT3	SNP	rs744166	PCR	MS	Disease risk	The combined evidence for association to STAT3 (rs744166) was significant.	N/A	20159113	Details
HLA-B	genotype	B55	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
IGH	N/A	IGHV3	PCR	MS	Disease risk	We find that all MOGspecific IgGκ Fab fragments, unrelated to genetic make-up, utilize a restricted set of variable region genes, IGHV1 and IGHV3 for the H chain and IGKV1, IGKV3, and IGKV5 for the L chain.	N/A	16528499	Details
CTLA4	CT60A/G	N/A	PCR	MS	Disease risk	We found that among the five polymorphisms studied, two (CT60A/G and Jo31G/T) were associated with susceptibility to MS.	We clearly show, for the first time, that 3′-UTR polymorphisms of the CTLA-4 gene influence both membrane and cytoplasmic CTLA-4 levels, as measured by MFI, and in this way they have impact on disease susceptibility.	19740340	Details
HLA-B	genotype	B56	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
IGKV@	N/A	IGKV1	PCR	MS	Disease risk	We find that all MOGspecific IgGκ Fab fragments, unrelated to genetic make-up, utilize a restricted set of variable region genes, IGHV1 and IGHV3 for the H chain and IGKV1, IGKV3, and IGKV5 for the L chain.	N/A	16528499	Details
TRB	Allele	NA	PCR	MS	Phenotypic risk	Susceptibility to RP MS is associated both with a recessive inheritance of a gene linked to the 30 (Vb11) end of the 2-1 subhaplotype defined by the Vb8-BamHI and Vb11-BamHI alleles in DRw151 patients and with a gene, located on the 1-1 subhaplotype, defined by the Vb1-TaqI and Vb8-MspI alleles of the TcR b-chain com-plex in DRw152 patients.	We tested the hypothesis that susceptibility to relapsing-progressive (RP) (but not to relapsing-remitting [RR])multiple sclerosis (MS) is associated with a gene linked to the TcR b-chain variable region delimited by the Vb8-BamHI and Vb11-BamHI RFLP alleles in DRw151 MS patients, using a contingency-table test of patient data and affected family–based controls.	9463308	Details
CTLA4	Jo31G/T	N/A	PCR	MS	Disease risk	We found that among the five polymorphisms studied, two (CT60A/G and Jo31G/T) were associated with susceptibility to MS.	We clearly show, for the first time, that 3′-UTR polymorphisms of the CTLA-4 gene influence both membrane and cytoplasmic CTLA-4 levels, as measured by MFI, and in this way they have impact on disease susceptibility.	19740340	Details
HLA-B	genotype	B59	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
IGKV@	N/A	IGKV3	PCR	MS	Disease risk	We find that all MOGspecific IgGκ Fab fragments, unrelated to genetic make-up, utilize a restricted set of variable region genes, IGHV1 and IGHV3 for the H chain and IGKV1, IGKV3, and IGKV5 for the L chain.	N/A	16528499	Details
CTLA4	SNP	CTLA-4-318, CTLA-4+49	PCR	MS	Disease risk	We found no association between carriership of any of the alleles either with susceptibility to MS or with clinical features and the polymorphisms under investigation do not affect the risk of developing MS and have no influence on the course of disease.	CTLA-4 may actually down regulate T cell function .	12864988	Details
IL1B	polymorphism	N/A	PCR	MS	Disease risk	IL-1beta gene polymorphisms may not be relevant in the susceptibility to MS or the clinical characteristics of Japanese patients with MS.	IL-1 is predominantly expressed by macrophages within the lesion centers and by microglia at and beyond the lesion edge. This expression of IL-1 may participate in the destruction of the central nervous system myelin.	11498264	Details
NOD2	Allele	NA	PCR	MS	Disease risk	Our results indicate that the NOD2 gene is probably not influencing susceptibility to autoimmune disease in general but is specific for Crohn’s disease.	During the last few years striking progress has been made in unravelling the genetic basis of susceptibility to Crohn’s disease. Significant evidence for linkage in the pericentromericc region of chromosome 16 has been found,3 fol-lowing on from which two independent groups, one using association mapping4 and the other following a candidate gene approach,5 identified the relevant gene as NOD2.	12876263	Details
CTLA4	CTLA-4-319C/T	N/A	PCR	MS	Disease risk	We found that among the five polymorphisms studied, two (CT60A/G and Jo31G/T) were associated with susceptibility to MS.	We clearly show, for the first time, that 3′-UTR polymorphisms of the CTLA-4 gene influence both membrane and cytoplasmic CTLA-4 levels, as measured by MFI, and in this way they have impact on disease susceptibility.	19740340	Details
HLA-B	genotype	B60	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
IGKV@	N/A	IGKV5	PCR	MS	Disease risk	We find that all MOGspecific IgGκ Fab fragments, unrelated to genetic make-up, utilize a restricted set of variable region genes, IGHV1 and IGHV3 for the H chain and IGKV1, IGKV3, and IGKV5 for the L chain.	N/A	16528499	Details
CD28	SNP	CD28-I3+17	PCR	MS	Disease risk	We found no association between carriership of any of the alleles either with susceptibility to MS or with clinical features and the polymorphisms under investigation do not affect the risk of developing MS and have no influence on the course of disease.	CD28 provides a signal essential for the initiation and progression of a T cell response.	12864988	Details
IL1RN	polymorphism	N/A	PCR	MS	Disease risk	IL-1ra gene polymorphisms may not be relevant in the susceptibility to MS or the clinical characteristics of Japanese patients with MS.	The IL-1 receptor antagonist ra protein is structurally related to IL-1b, and competes with IL-1b for the IL-1 receptor, thereby preventing activation of the target cells.	11498264	Details
HLA-A	Allele	NA	PCR	MS	Disease risk	We found both class I (A, Cw, B) and class II (DR, DQ) loci to have an effect on MS susceptibility, but we saw that they act independently from each other.	The human leukocyte antigen (HLA) complex on chromosome 6p21 has been unambiguously associated with multiple sclerosis (MS)	19654877	Details
CTLA4	(AT)n repeat	N/A	PCR	MS	Disease risk	We found that among the five polymorphisms studied, two (CT60A/G and Jo31G/T) were associated with susceptibility to MS.	We clearly show, for the first time, that 3′-UTR polymorphisms of the CTLA-4 gene influence both membrane and cytoplasmic CTLA-4 levels, as measured by MFI, and in this way they have impact on disease susceptibility.	19740340	Details
HLA-B	genotype	B61	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
IL10	polymorphism	IL-10R2	PCR	MS	Disease risk	No other allele showed a significant difference between patients and controls, and the TDT analysis yielded negative results.	N/A	12458048	Details
CYP27B1	SNP	rs11574010	PCR	MS	Disease risk	a significant interaction was observed between winter sun exposure during childhood, genotype at rs11574010	the vitamin D hormonal pathway	19383647	Details
HLA-C	Allele	NA	PCR	MS	Disease risk	We found both class I (A, Cw, B) and class II (DR, DQ) loci to have an effect on MS susceptibility, but we saw that they act independently from each other.	The human leukocyte antigen (HLA) complex on chromosome 6p21 has been unambiguously associated with multiple sclerosis (MS)	19654877	Details
HLA-B	genotype	B62	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
IL10	polymorphism	IL-10R3	PCR	MS	Disease risk	No other allele showed a significant difference between patients and controls, and the TDT analysis yielded negative results.	N/A	12458048	Details
CYP27B1	SNP	rs10735810	PCR	MS	Disease risk	No significant interactions were observed for either rs10735810 or rs731236, after stratification by sun exposure	the vitamin D hormonal pathway	19383647	Details
HLA-B	Allele	NA	PCR	MS	Disease risk	We found both class I (A, Cw, B) and class II (DR, DQ) loci to have an effect on MS susceptibility, but we saw that they act independently from each other.	The human leukocyte antigen (HLA) complex on chromosome 6p21 has been unambiguously associated with multiple sclerosis (MS)	19654877	Details
TNFRSF1A	R92Q	N/A	PCR	MS	Disease risk	The penetrance of the R92Q mutation in affected family members was higher than reported. We recommend careful observation of MS patients with coexisting TRAPS with regard to unexpected side effects of immunomodulatory therapies.	N/A	19029521	Details
HLA-B	genotype	B67	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
CTSS	SNP	rs2275235a	PCR	MS	Phenotype risk	Additionally, we recorded nominally significant associations of response with five other genes, MBP, CD86, FAS, IL1R1 and IL12RB2, which are likely to be involved in glatiramer acetate’s modeof-action, both directly and indirectly.	N/A	17622942	Details
IL10	polymorphism	IL-10R4	PCR	MS	Disease risk	No other allele showed a significant difference between patients and controls, and the TDT analysis yielded negative results.	N/A	12458048	Details
CYP27B1	SNP	rs731236	PCR	MS	Disease risk	No significant interactions were observed for either rs10735810 or rs731236, after stratification by sun exposure	the vitamin D hormonal pathway	19383647	Details
HLA-DRA	Allele	NA	PCR	MS	Disease risk	We found both class I (A, Cw, B) and class II (DR, DQ) loci to have an effect on MS susceptibility, but we saw that they act independently from each other.	The human leukocyte antigen (HLA) complex on chromosome 6p21 has been unambiguously associated with multiple sclerosis (MS)	19654877	Details
HLA-B	genotype	B70	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
CTSS	SNP	rs1415148a	PCR	MS	Phenotype risk	Additionally, we recorded nominally significant associations of response with five other genes, MBP, CD86, FAS, IL1R1 and IL12RB2, which are likely to be involved in glatiramer acetate’s modeof-action, both directly and indirectly.	N/A	17622942	Details
IL10	polymorphism	IL-10G7	PCR	MS	Disease risk	No other allele showed a significant difference between patients and controls, and the TDT analysis yielded negative results.	N/A	12458048	Details
ICAM1	Gene polymorphisms	ICAM1 AA	PCR	MS	Disease risk	An increased risk for the AA (Lys(469)/Lys(469)) genotype was found in both populations	sequence variations in the ICAM-1 gene could potentially be responsible for the genetic susceptibility to MS	12590979	Details
HLA-DRB1	Allele	NA	PCR	MS	Disease risk	We found both class I (A, Cw, B) and class II (DR, DQ) loci to have an effect on MS susceptibility, but we saw that they act independently from each other.	The human leukocyte antigen (HLA) complex on chromosome 6p21 has been unambiguously associated with multiple sclerosis (MS)	19654877	Details
HLA-B	genotype	B75	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
TRB	SNP	rs71878b	PCR	MS	Phenotype risk	Additionally, we recorded nominally significant associations of response with five other genes, MBP, CD86, FAS, IL1R1 and IL12RB2, which are likely to be involved in glatiramer acetate’s modeof-action, both directly and indirectly.	N/A	17622942	Details
IL10	polymorphism	IL-10G8	PCR	MS	Disease risk	No other allele showed a significant difference between patients and controls, and the TDT analysis yielded negative results.	N/A	12458048	Details
ICAM1	Gene polymorphisms	ICAM1 AA	PCR	MS	Disease risk	An increased risk for the AA (Lys(469)/Lys(469)) genotype was found in both populations	sequence variations in the ICAM-1 gene could potentially be responsible for the genetic susceptibility to MS	12590979	Details
HLA-DQA1	Allele	NA	PCR	MS	Disease risk	We found both class I (A, Cw, B) and class II (DR, DQ) loci to have an effect on MS susceptibility, but we saw that they act independently from each other.	The human leukocyte antigen (HLA) complex on chromosome 6p21 has been unambiguously associated with multiple sclerosis (MS)	19654877	Details
UCP2	UCP2-866G	N/A	PCR	MS	Disease risk	Thus, UCP2 promoter polymorphism may contribute to MS susceptibility by regulating the level of UCP2 protein in the central nervous and/or the immune systems.	N/A	16021520	Details
HLA-B	genotype	Bw4	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
MBP	SNP	rs470929a	PCR	MS	Phenotype risk	Additionally, we recorded nominally significant associations of response with five other genes, MBP, CD86, FAS, IL1R1 and IL12RB2, which are likely to be involved in glatiramer acetate’s modeof-action, both directly and indirectly.	N/A	17622942	Details
IL10	polymorphism	IL-10G9	PCR	MS	Disease risk	No other allele showed a significant difference between patients and controls, and the TDT analysis yielded negative results.	N/A	12458048	Details
IFNAR1	SNP	ref.27	PCR	MS	Treatment risk	In addition, no significant association was observed of any of the IFNAR gene polymorphisms with susceptibility to MS, as studied by a family-based association analysis	Interferon beta (IFNbeta) has been shown to decrease clinical relapses, reduce brain disease activity	12618863	Details
HLA-DQB1	Allele	NA	PCR	MS	Disease risk	We found both class I (A, Cw, B) and class II (DR, DQ) loci to have an effect on MS susceptibility, but we saw that they act independently from each other.	The human leukocyte antigen (HLA) complex on chromosome 6p21 has been unambiguously associated with multiple sclerosis (MS)	19654877	Details
HLA-B	genotype	Bw6	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
CD86	SNP	rs2001791a	PCR	MS	Phenotype risk	Additionally, we recorded nominally significant associations of response with five other genes, MBP, CD86, FAS, IL1R1 and IL12RB2, which are likely to be involved in glatiramer acetate’s modeof-action, both directly and indirectly.	N/A	17622942	Details
IL10	polymorphism	IL-10G10	PCR	MS	Disease risk	No other allele showed a significant difference between patients and controls, and the TDT analysis yielded negative results.	N/A	12458048	Details
APOE	allele	epsilon4 Allele positive / negative	PCR	MS	Disease risk	No association between the APOE epsilon4 allele and outcome and susceptibility in primary progressive multiple sclerosis.	The epsilon class of APOE is involved in lipid transport and plays a part in brain development, synapse repair, and response to neuronal injury.	10847793	Details
HLA-DRB1	alleles	N/A	PCR	MS	Disease risk	We identified two previously unknown MS-associated tri-allelic combinations: -509TGFβ1*C, DRB1*18(3), CTLA4*G and -238TNF*B1,-308TNF*A2, CTLA4*G, which perfectly separate MS cases from controls, at least in the present sample. The previously described DRB1*15(2) allele, the microsatellite TNFa9 allele and the biallelic combination CCR5Δ32, DRB1*04 were also reidentified as MS-associated	tri-allelic combinations	16872485	Details
IFNAR1	SNP	rs1041429	PCR	MS	Treatment risk	In addition, no significant association was observed of any of the IFNAR gene polymorphisms with susceptibility to MS, as studied by a family-based association analysis	Interferon beta (IFNbeta) has been shown to decrease clinical relapses, reduce brain disease activity	12618863	Details
GRM7	SNP	rs779867	PCR	MS	Disease risk	The rs779867 was associated with MS risk in recessive model (OR (95% CI) = 0.67 (0.48–0.94)), P-value = 0.02, adjusted P-value = 0.04).	Glutamate excitotoxicity has been previously associated with development of multiple sclerosis (MS). The me-tabotropic glutamate receptor 7 (GRM7) gene is a G protein-coupled receptor that suppresses the cyclic AMP cascade after activation by glutamate.	30616226	Details
IFNGR2	IFNGR2*Arg64	N/A	PCR	MS	Disease risk	The IFNGR1 and IFNGR2 gene polymorphisms studied do not exert an important influence on MS susceptibility, but allele IFNGR2*Arg64 may be associated with a progressive disease onset.	N/A	15182327	Details
HLA-C	genotype	Cw1	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
CD86	SNP	1129055a	PCR	MS	Phenotype risk	Additionally, we recorded nominally significant associations of response with five other genes, MBP, CD86, FAS, IL1R1 and IL12RB2, which are likely to be involved in glatiramer acetate’s modeof-action, both directly and indirectly.	N/A	17622942	Details
IL10	polymorphism	IL-10G11	PCR	MS	Disease risk	No other allele showed a significant difference between patients and controls, and the TDT analysis yielded negative results.	N/A	12458048	Details
NR3C1	SNP	N/A	PCR	MS	Treatment risk	No significant difference in the mutation distribution was detected between the responders and non-responders to GC therapy.	GC is the first-line therapy in acute attack of MS, and GR plays a critical role in the therapeutic effects of GC. Several GR gene polymorphisms have been reported to be associated with either glucocorticoid hypersensitivity or glucocorticoid resistance in various diseases.	32277392	Details
TNF	alleles	N/A	PCR	MS	Disease risk	We identified two previously unknown MS-associated tri-allelic combinations: -509TGFβ1*C, DRB1*18(3), CTLA4*G and -238TNF*B1,-308TNF*A2, CTLA4*G, which perfectly separate MS cases from controls, at least in the present sample. The previously described DRB1*15(2) allele, the microsatellite TNFa9 allele and the biallelic combination CCR5Δ32, DRB1*05 were also reidentified as MS-associated	tri-allelic combinations	16872485	Details
IFNAR1	SNP	rs1012334	PCR	MS	Treatment risk	In addition, no significant association was observed of any of the IFNAR gene polymorphisms with susceptibility to MS, as studied by a family-based association analysis	Interferon beta (IFNbeta) has been shown to decrease clinical relapses, reduce brain disease activity	12618863	Details
GRM7	SNP	rs6782011	PCR	MS	Disease risk	There was no significant difference in allele and genotype frequencies of rs6782011 between cases and controls.	Glutamate excitotoxicity has been previously associated with development of multiple sclerosis (MS). The me-tabotropic glutamate receptor 7 (GRM7) gene is a G protein-coupled receptor that suppresses the cyclic AMP cascade after activation by glutamate.	30616226	Details
APOE	epsilon4	N/A	PCR	MS	Disease risk	The presence of significant NBV decreases only in the group of RRMS patients with the ApoE epsilon4 genotype provides new evidence that links ApoE epsilon4-related impaired mechanisms of cell repair and severe tissue destruction in MS.	Results of the present study suggest that this negative influence of the ApoE epsilon4 genotype might be active from the earliest disease stages.	10864599	Details
HLA-C	genotype	Cw3	PCR	MS	Disease risk	We found significant associations with HLA-Cw3 (p -- 0.002, Pc = 0.012, RR = 3.2), DR2 (p = 0.007, RR = 2.6), and DQBI*0602 (p = 0.04, RR = 4.0) in Japanese patients for the first time.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
IL1R1	SNP	rs956730a	PCR	MS	Phenotype risk	Additionally, we recorded nominally significant associations of response with five other genes, MBP, CD86, FAS, IL1R1 and IL12RB2, which are likely to be involved in glatiramer acetate’s modeof-action, both directly and indirectly.	N/A	17622942	Details
IL10	polymorphism	IL-10G12	PCR	MS	Disease risk	IL-10G12 allele was significantly increased in MS patients.	N/A	12458048	Details
TGFB1	alleles	N/A	PCR	MS	Disease risk	We identified two previously unknown MS-associated tri-allelic combinations: -509TGFβ1*C, DRB1*18(3), CTLA4*G and -238TNF*B1,-308TNF*A2, CTLA4*G, which perfectly separate MS cases from controls, at least in the present sample. The previously described DRB1*15(2) allele, the microsatellite TNFa9 allele and the biallelic combination CCR5Δ32, DRB1*06 were also reidentified as MS-associated	tri-allelic combinations	16872485	Details
IFNAR1	SNP	rs1012335	PCR	MS	Treatment risk	In addition, no significant association was observed of any of the IFNAR gene polymorphisms with susceptibility to MS, as studied by a family-based association analysis	Interferon beta (IFNbeta) has been shown to decrease clinical relapses, reduce brain disease activity	12618863	Details
GRM7	SNP	rs779867	PCR	MS	Disease risk	None of the estimated haplotype blocks of rs6782011 and rs779867 were associated with MS risk in the assessed population.	N/A	30616226	Details
FCGR2A	allele	N/A	PCR	MS	N/A	The allele frequencies of the FcgammaRIIA and FcgammaRIIIB did not differ significantly between the MS patients and the controls.	FcgammaRIIIB NA1/NA1 and FcgammaRIIA H/H bind more efficient IgG1/IgG3 and IgG2 subclasses, respectively, than FcgammaRIIIB NA2/NA2 and FcgammaRIIA R/R. A more effective processing of circulating immune complexes may be one mechanism for better clinical outcome in MS.	10371522	Details
HLA-C	genotype	Cw9	PCR	MS	Disease risk	The frequencies of Cw9 and Cwl0 were 38.6% and 27.3%, respectively, which were not significantly different from the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
FAS	SNP	rs982764a	PCR	MS	Phenotype risk	Additionally, we recorded nominally significant associations of response with five other genes, MBP, CD86, FAS, IL1R1 and IL12RB2, which are likely to be involved in glatiramer acetate’s modeof-action, both directly and indirectly.	N/A	17622942	Details
IL10	polymorphism	IL-10G13	PCR	MS	Disease risk	No other allele showed a significant difference between patients and controls, and the TDT analysis yielded negative results.	N/A	12458048	Details
CFH	allele-haplotype	Tyr402	PCR	MS	Disease risk	There was no significant difference in the frequency of CFH Tyr402 His genotypes and alleles between MS patients and healthy controls.	Serum CFH is the major fluid-phase regulator of the alternative pathway of C, increasingly recognised as a critical player in many diseases.	26186240	Details
CTLA4	alleles	N/A	PCR	MS	Disease risk	We identified two previously unknown MS-associated tri-allelic combinations: -509TGFβ1*C, DRB1*18(3), CTLA4*G and -238TNF*B1,-308TNF*A2, CTLA4*G, which perfectly separate MS cases from controls, at least in the present sample. The previously described DRB1*15(2) allele, the microsatellite TNFa9 allele and the biallelic combination CCR5Δ32, DRB1*07 were also reidentified as MS-associated	tri-allelic combinations	16872485	Details
IFNAR1	SNP	rs2257167	PCR	MS	Treatment risk	In addition, no significant association was observed of any of the IFNAR gene polymorphisms with susceptibility to MS, as studied by a family-based association analysis	Interferon beta (IFNbeta) has been shown to decrease clinical relapses, reduce brain disease activity	12618863	Details
GRM7	SNP	rs6782011	PCR	MS	Disease risk	None of the estimated haplotype blocks of rs6782011 and rs779867 were associated with MS risk in the assessed population.	Tumor necrosis factor (TNF)-a and TNF-b are proinflammatory cytokines that have been implicated in the pathogenesis of several autoimmune diseases	12568117	Details
FCGR3B	allele	N/A	PCR	MS	N/A	The allele frequencies of the FcgammaRIIA and FcgammaRIIIB did not differ significantly between the MS patients and the controls.	FcgammaRIIIB NA1/NA1 and FcgammaRIIA H/H bind more efficient IgG1/IgG3 and IgG2 subclasses, respectively, than FcgammaRIIIB NA2/NA2 and FcgammaRIIA R/R. A more effective processing of circulating immune complexes may be one mechanism for better clinical outcome in MS.	10371522	Details
HLA-C	genotype	Cw10	PCR	MS	Disease risk	The frequencies of Cw9 and Cwl0 were 38.6% and 27.3%, respectively, which were not significantly different from the controls.	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
TRB	SNP	rs71878c	PCR	MS	Phenotype risk	Additionally, we recorded nominally significant associations of response with five other genes, MBP, CD86, FAS, IL1R1 and IL12RB2, which are likely to be involved in glatiramer acetate’s modeof-action, both directly and indirectly.	N/A	17622942	Details
IL10	polymorphism	IL-10G14	PCR	MS	Disease risk	No other allele showed a significant difference between patients and controls, and the TDT analysis yielded negative results.	N/A	12458048	Details
CCR5	alleles	N/A	PCR	MS	Disease risk	We identified two previously unknown MS-associated tri-allelic combinations: -509TGFβ1*C, DRB1*18(3), CTLA4*G and -238TNF*B1,-308TNF*A2, CTLA4*G, which perfectly separate MS cases from controls, at least in the present sample. The previously described DRB1*15(2) allele, the microsatellite TNFa9 allele and the biallelic combination CCR5Δ32, DRB1*08 were also reidentified as MS-associated	tri-allelic combinations	16872485	Details
IFNAR2	SNP	rs3153	PCR	MS	Treatment risk	In addition, no significant association was observed of any of the IFNAR gene polymorphisms with susceptibility to MS, as studied by a family-based association analysis	Interferon beta (IFNbeta) has been shown to decrease clinical relapses, reduce brain disease activity	12618863	Details
LTA	Allele	NA	PCR	MS	Disease risk	These results suggest that the TNF-b gene plays a significant role in the etiopathogenesis of MS.	Tumor necrosis factor (TNF)-a and TNF-b are proinflammatory cytokines that have been implicated in the pathogenesis of several autoimmune diseases	12568117	Details
CTLA4	intragenic polymorphisms	N/A	PCR	MS	Disease risk	We observed a significant association (p < 0.05) for homozygosity for the G49 allele in a case-control analysis of 378 MS patients and 237 controls, and a transmission disequilibrium (p < 0.02) for the G49 allele in 31 MS families. This was further corroborated by evidence for linkage by the affected pedigree member (APM) analysis (p < 0.0002) and a transmission distortion (p < 0.05) of the exon 4(642) polymorphism.	Our results suggest that a dysregulation of CTLA-4-driven downregulation of T-cell activation could be involved in the pathogenesis of MS.	10408973	Details
HLA-C	genotype	Cw4	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
Tcrb	polymorphisms	Vβ8.2	PCR	EAE	Disease risk	In EAE-recovered mice, certain myelin basic protein-reactive CD4βV8.2β clones are significantly decreased and this decrease is not observed if CD8β T cells were depleted from these mice.	N/A	12824465	Details
IL12RB2	SNP	rs946685c	PCR	MS	Phenotype risk	Additionally, we recorded nominally significant associations of response with five other genes, MBP, CD86, FAS, IL1R1 and IL12RB2, which are likely to be involved in glatiramer acetate’s modeof-action, both directly and indirectly.	N/A	17622942	Details
IL10	polymorphism	IL-10G15	PCR	MS	Disease risk	No other allele showed a significant difference between patients and controls, and the TDT analysis yielded negative results.	N/A	12458048	Details
HLA-DRB1	genotype	DRB1*1501-DQA1*0102-DQB1* 0602 (DR15)	PCR	MS	Disease risk	This suggests that DR15 exerts a susceptibility rather than disease modifying effect in multiple sclerosis.	N/A	11796767	Details
MIF	SNP	173 G/C	PCR	MS	Phenotypic risk	The frequency of the 173 C-containing allele, was significantly underrepresented in RRMS subjects with disease duration of more than 10 or 15 year compared with progressive MS subjects.	MIF was one of the first cytokines to be described and is a key mediator of many autoimmune inflammatory diseases.It was suggested that MIF contributes to the pathogenesis of EAE/MS by promoting leukocyte recruitment into the CNS, inhibiting apoptosis of activated monocytes, and enhancing the secretion of proinflammatory cytokines.	28923927	Details
IFNAR2	SNP	rs1051393	PCR	MS	Treatment risk	In addition, no significant association was observed of any of the IFNAR gene polymorphisms with susceptibility to MS, as studied by a family-based association analysis	Interferon beta (IFNbeta) has been shown to decrease clinical relapses, reduce brain disease activity	12618863	Details
TNF	Allele	NA	PCR	MS	Disease risk	TNF-α genotypes were not associated with MS	Tumor necrosis factor (TNF)-a and TNF-b are proinflammatory cytokines that have been implicated in the pathogenesis of several autoimmune diseases	12568117	Details
HLA-C	genotype	Cw5	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DRB1	polymorphisms	DRB1*01	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
HLA-DQA1	genotype	DRB1*1501-DQA1*0102-DQB1* 0602 (DR15)	PCR	MS	Disease risk	This suggests that DR15 exerts a susceptibility rather than disease modifying effect in multiple sclerosis.	N/A	11796767	Details
DDT	polymorphism	rs5844572(794 CATT5–8)	PCR	MS	Phenotypic risk	The frequency of the 794 CATT7 or the high-expression 794 CATT8-containing genotype alone also was lower in RRMS subjects with long disease duration compared with progressive MS subjects.	D-DT has a neuroinflammatory role and similarly affects cell migration.	28923927	Details
IFNAR2	SNP	rs1131668	PCR	MS	Treatment risk	In addition, no significant association was observed of any of the IFNAR gene polymorphisms with susceptibility to MS, as studied by a family-based association analysis	Interferon beta (IFNbeta) has been shown to decrease clinical relapses, reduce brain disease activity	12618863	Details
CD226	SNP	rs763361	PCR	MS	Disease risk	The Ser307 allele of rs763361 in exon 7 of CD226 predisposes to T1D,MS, possibly AITD and possibly RA, and based on the tag SNP analysis, could be the causal variant.	We previously reported association of a nonsynonymous single nucleotide polymorphism (nsSNP) rs763361/Gly307Ser in the immune response gene CD226 on chromosome 18q22 with type 1 diabetes (T1D) susceptibility.	18971939	Details
HLA-C	genotype	Cw6	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DRB1	polymorphisms	DRB1*03	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
HLA-DQB1	genotype	DRB1*1501-DQA1*0102-DQB1* 0602 (DR15)	PCR	MS	Disease risk	This suggests that DR15 exerts a susceptibility rather than disease modifying effect in multiple sclerosis.	N/A	11796767	Details
CASP9	Gene polymorphisms	CASP9 G/G	PCR	MS	Disease risk	Our results suggest that the presence of the G/G genotype represents a higher risk factor in our MS population and a differential production of CASP-9 might be a contributory factor in determining the severity of MS	Caspase-9 is a primary effector CASP that executes programmed cell death, which plays an important role in the development of multiple sclerosis	19359048	Details
APOE	Allele	NA	PCR	MS	Disease risk	This study does not support a role for the epsilon4 allele in cognitive dysfunction in multiple sclerosis.	Evidence linking APOE to myelin repair, neuronal plasticity, and cerebral inflammatory processes suggests that it may be relevant in multiple sclerosis (MS).	20479360	Details
HLA-C	genotype	Cw7	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DRB1	polymorphisms	DRB1*04	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
HLA-DRB1	genotype	DRB1*1501-DQA1*0102-DQB1* 0602 (DR15)	PCR	MS	Phenotypic risk	This suggests that DR15 exerts a susceptibility rather than disease modifying effect in multiple sclerosis.	N/A	11796767	Details
HLA-DRB1	allele	*1501,*0301,*0701,*1104,*0102	PCR	MS	Phenotypic risk	DRB1*1501 is associated with diffuse lesions.DRB1*1501 homozygosity was significantly more likely in cases with diffuse lesions than non-carriage of DRB1*1501 or DRB1*1501 heterozygosity and the proportion of cases with diffuse lesions was higher amongst heterozygous DRB1*1501 carriers.Among those with focal lesions carriage of DRB1*1104 was associated with higher total numbers of lesions.In multivariable analysis DRB1*0701 and DRB1*1104mwere independently associated with higher total lesion numbers compared with carriage of other alleles.DRB1*1501 and DRB1*1101 were significantly associated with greater lesion length.When combined to the 2 digit DRB1*11, there was a significant association between this allele group and lesion length .DRB1*0102,DRB1*0103 and DRB1*1104 were separately associated with numbers of thoracic cord lesions,DRB1*0103 with reduced numbers and the other alleles with increased numbers. DRB1*1104 was positively associated with thoracic cord lesion numbers and DRB1*0103 negatively correlated.	The biological mechanisms which underlie these effects remain speculative but may be due to regional differences in the levels of expression of MHC Class II antigens and the presentation of myelin antigens to the immune system.	20884011	Details
RORA	SNP	rs4774388	PCR	MS	Treatment risk	The obtained result of the current study showed a significant association between nonresponsiveness and the rs4774388 in dominant model	The obtained results of the present study suggested the rs4774388 as a possible effective factor in determination of response to IFN-β	31649263	Details
HLA-DRA	Allele	NA	PCR	MS	Disease risk	An MS-associated and linked series of allele-specific RFLPs or allogenotypes was identified among this relatively homogeneous ethnic group; the allogenotypes include DRwl5, DQw6 and a DQA1 allogenotype termed DQalb. An additional allogenotype which cross-hybridizes with DQA1 and is termed DQA2 upper (DQA2U), was shown not only to be part of the MS-associated extended haplotype, but also to be independently associated with MS in DRwl5-nega-tive patients. Conversely a second DQA2 allogenotype, termed DQA2 lower (DQA2L) and a DQB1 allogenotype (DQw7) linked to DQA2L showed negative correlations with MS. It seems likely that the relationship of the HLA class II gene region to MS is complex and that MS susceptibility may reflect interaction between disease susceptibility and resistance genes.	HLA class II DRBI, DQB1 and DQA1 gene probes were used to study DNA from unrelated French	2125855	Details
HLA-C	genotype	Cw11	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DRB1	polymorphisms	DRB1*07	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
HLA-DQA1	genotype	DRB1*1501-DQA1*0102-DQB1* 0602 (DR15)	PCR	MS	Phenotypic risk	This suggests that DR15 exerts a susceptibility rather than disease modifying effect in multiple sclerosis.	N/A	11796767	Details
RORA	SNP	rs11639084	PCR	MS	Treatment risk	However, the allele and genotype frequencies of rs11639084 were not different between controls, nonresponder, and responder patients	The obtained results of the present study suggested the rs4774388 as a possible effective factor in determination of response to IFN-β	31649263	Details
HLA-DRB1	Allele	NA	PCR	MS	Disease risk	An MS-associated and linked series of allele-specific RFLPs or allogenotypes was identified among this relatively homogeneous ethnic group; the allogenotypes include DRwl5, DQw6 and a DQA1 allogenotype termed DQalb. An additional allogenotype which cross-hybridizes with DQA1 and is termed DQA2 upper (DQA2U), was shown not only to be part of the MS-associated extended haplotype, but also to be independently associated with MS in DRwl5-nega-tive patients. Conversely a second DQA2 allogenotype, termed DQA2 lower (DQA2L) and a DQB1 allogenotype (DQw7) linked to DQA2L showed negative correlations with MS. It seems likely that the relationship of the HLA class II gene region to MS is complex and that MS susceptibility may reflect interaction between disease susceptibility and resistance genes.	HLA class II DRBI, DQB1 and DQA1 gene probes were used to study DNA from unrelated French	2125855	Details
HLA-C	genotype	Blank (double)'	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DRB1	polymorphisms	DRB1*08	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
HLA-DQB1	genotype	DRB1*1501-DQA1*0102-DQB1* 0602 (DR15)	PCR	MS	Phenotypic risk	This suggests that DR15 exerts a susceptibility rather than disease modifying effect in multiple sclerosis.	N/A	11796767	Details
Ccl1	gene Polymorphism	N/A	PCR	EAE	Disease risk	these sequence polymorphisms are promising candidates for eae7, a locus associated with severity of clinical signs and susceptibility to the shorter, less severe monophasic remitting/nonrelapsing form of disease.	multiple sequence polymorphisms resulting in signicant amino acid substitutions were identied in Scya1 (TCA-3), Scya2 (monocyte chemoattractant protein (MCP)-1), and Scya12 (MCP-5)	10438970	Details
DBP	Gene polymorphisms	codon 416	PCR	MS	Disease risk	no association was observed between the DBP polymorphisms and the age at disease onset	These results suggest that DBP does not contribute to the development of MS in Japanese	12044990	Details
HLA-DQA1	Allele	NA	PCR	MS	Disease risk	An MS-associated and linked series of allele-specific RFLPs or allogenotypes was identified among this relatively homogeneous ethnic group; the allogenotypes include DRwl5, DQw6 and a DQA1 allogenotype termed DQalb. An additional allogenotype which cross-hybridizes with DQA1 and is termed DQA2 upper (DQA2U), was shown not only to be part of the MS-associated extended haplotype, but also to be independently associated with MS in DRwl5-nega-tive patients. Conversely a second DQA2 allogenotype, termed DQA2 lower (DQA2L) and a DQB1 allogenotype (DQw7) linked to DQA2L showed negative correlations with MS. It seems likely that the relationship of the HLA class II gene region to MS is complex and that MS susceptibility may reflect interaction between disease susceptibility and resistance genes.	HLA class II DRBI, DQB1 and DQA1 gene probes were used to study DNA from unrelated French	2125855	Details
HLA-C	genotype	Blank (single) d	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DRB1	polymorphisms	DRB1*09	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
NFKBIA	SNP	rs3138053	PCR	MS	Disease risk	The genotype frequencies of IκBα-881A/G and allele frequencies of IκBα-881G were significantly higher in patients with MS with respect to as compared to the controls.	NF-kB plays a substantial role in inflammatory diseases and in the development of autoimmunity such as multiple sclerosis .The anti-apoptogenic effect of NF-jB is well documented. Inhibitor of kappa B (IkB) is an inhibitor of NF-kB, which binds withNF-kB in the cytoplasm and controls the transcriptional activity of NF-kB.	24368589	Details
Mcpt1	gene Polymorphism	N/A	PCR	EAE	Disease risk	these sequence polymorphisms are promising candidates for eae7, a locus associated with severity of clinical signs and susceptibility to the shorter, less severe monophasic remitting/nonrelapsing form of disease.	multiple sequence polymorphisms resulting in signicant amino acid substitutions were identied in Scya1 (TCA-3), Scya2 (monocyte chemoattractant protein (MCP)-1), and Scya12 (MCP-5)	10438970	Details
DBP	Gene polymorphisms	codon 420	PCR	MS	Disease risk	no association was observed between the DBP polymorphisms and the age at disease onset	These results suggest that DBP does not contribute to the development of MS in Japanese	12044990	Details
HLA-DQB1	Allele	NA	PCR	MS	Disease risk	An MS-associated and linked series of allele-specific RFLPs or allogenotypes was identified among this relatively homogeneous ethnic group; the allogenotypes include DRwl5, DQw6 and a DQA1 allogenotype termed DQalb. An additional allogenotype which cross-hybridizes with DQA1 and is termed DQA2 upper (DQA2U), was shown not only to be part of the MS-associated extended haplotype, but also to be independently associated with MS in DRwl5-nega-tive patients. Conversely a second DQA2 allogenotype, termed DQA2 lower (DQA2L) and a DQB1 allogenotype (DQw7) linked to DQA2L showed negative correlations with MS. It seems likely that the relationship of the HLA class II gene region to MS is complex and that MS susceptibility may reflect interaction between disease susceptibility and resistance genes.	HLA class II DRBI, DQB1 and DQA1 gene probes were used to study DNA from unrelated French	2125855	Details
HLA-DRB1	genotype	DR1	PCR	MS	Disease risk	Frequencies of HLA-A, B, C in 44 MS patients and 98 controls	These results suggest that MS susceptibility may result from polygenic influences and from the presence of environmental factors.	1286977	Details
HLA-DRB1	polymorphisms	DRB1*010	PCR	MS	Treatment risk	HLA genotype does not appear to influence the clinical response to IFN-b in MS patients.	N/A	16281922	Details
NFKBIA	SNP	rs2233406	PCR	MS	Disease risk	The genotype frequencies of IκBα-826T/T was significantly higher in patients with MS with respect to as compared to the controls.	NF-kB plays a substantial role in inflammatory diseases and in the development of autoimmunity such as multiple sclerosis .The anti-apoptogenic effect of NF-jB is well documented. Inhibitor of kappa B (IkB) is an inhibitor of NF-kB, which binds withNF-kB in the cytoplasm and controls the transcriptional activity of NF-kB.	24368589	Details
Ccl12	gene Polymorphism	N/A	PCR	EAE	Disease risk	these sequence polymorphisms are promising candidates for eae7, a locus associated with severity of clinical signs and susceptibility to the shorter, less severe monophasic remitting/nonrelapsing form of disease.	multiple sequence polymorphisms resulting in signicant amino acid substitutions were identied in Scya1 (TCA-3), Scya2 (monocyte chemoattractant protein (MCP)-1), and Scya12 (MCP-5)	10438970	Details
IL4R	Gene polymorphisms	R551	PCR	MS	Disease risk	However, further analysis of all 341 MS patients did not confirm the finding that this IL4R variant represents a general genetic risk factor for MS .After correction for multiple comparisons only the genotype differences between PPMS patients and healthy controls remained statistically significant	nalysis of the first 100 MS patients for six IL4R variants showed an increased frequency of the R551 variant in MS patients versus healthy controls and carriage of the same IL4R variant was weakly associated with myelin oligodendrocyte glycoprotein (MOG) autoantibody production	11164908	Details
HLA-DQA2	Allele	NA	PCR	MS	Disease risk	An MS-associated and linked series of allele-specific RFLPs or allogenotypes was identified among this relatively homogeneous ethnic group; the allogenotypes include DRwl5, DQw6 and a DQA1 allogenotype termed DQalb. An additional allogenotype which cross-hybridizes with DQA1 and is termed DQA2 upper (DQA2U), was shown not only to be part of the MS-associated extended haplotype, but also to be independently associated with MS in DRwl5-nega-tive patients. Conversely a second DQA2 allogenotype, termed DQA2 lower (DQA2L) and a DQB1 allogenotype (DQw7) linked to DQA2L showed negative correlations with MS. It seems likely that the relationship of the HLA class II gene region to MS is complex and that MS susceptibility may reflect interaction between disease susceptibility and resistance genes.	HLA class II DRBI, DQB1 and DQA1 gene probes were used to study DNA from unrelated French	2125855	Details
RORA	SNP	rs11639048	4P-ARMS-PCR	MS	Disease risk	In the present study we investigated the effect of the rs11639048 and rs4774388 SNPs in the RORΑ gene on individual susceptibility to MS.	N/A	27653902	Details
RORA	SNP	rs4774388	4P-ARMS-PCR	MS	Disease risk	In the present study we investigated the effect of the rs11639048 and rs4774388 SNPs in the RORΑ gene on individual susceptibility to MS.	N/A	27653902	Details
HLA-A	haplotype	N/A	a commercial kit (LABType SSO Typing Tests),alleles’ detection was done using a non-radioactive PCR-SSOP (polymerase chain reaction-based sequence specific oligonucleotide probe) reverse line-blot assay,	MS	Disease risk	The OR for HLA-A *30 was 7.2 (95%CI:.74, 70.2) times the odds of having MS in participants classified in the category “others”. This excess was marginally significant (p-value= 0.089).	N/A	23767380	Details
HLA-DRB1	haplotype	N/A	a commercial kit (LABType SSO Typing Tests),alleles’ detection was done using a non-radioactive PCR-SSOP (polymerase chain reaction-based sequence specific oligonucleotide probe) reverse line-blot assay,	MS	Disease risk	The odds of having MS in participants with allele HLA-DRB1 *01 was 11.0 (95%CI: 1.1, 109.7) times the odds of having MS in participants classified in the category “others”. This excess was statistically significant (p-value= 0.041).The odds of having MS in participants with allele *03 was 4.3 (95%CI: 0.97, 19.1) times the odds of having MS in participants classified in the category “others”.his excess was marginally significant (p-value=0.054).The odds of having MS in participants with allele *04 was 0.23 (95%CI: 0.05, 1.09) lower than the odds of having MS in participants with allele *02. This excess was marginally significant (p-value=0.066).	N/A	23767380	Details
HLA-DRB1	SNP	HLA-DRB1*15 allele(DRB1*01,DRB1*03,DRB1*04)	a low-resolution sequence-specific PCR amplification method	MS	Treatment risk	The HLA-DRB1*15 allele in patients with MS had a statistically significant higher frequency when compared with controls.In the univariate analysis, the DRB1*01 and DRB1*04 alleles were associated with a worse prognosis , whereas the DRB1*03 was correlated with a better outcome.In the multivariate analysis, the alleles*01 and *04 were demonstrated to be independent factors to have a worse prognosis.	N/A	20629714	Details
RT1-A3	haplotype	N/A	a microsatellite marker located within the RT1 region	EAE	Phenotypic risk	MHC haplotypes differ in the severity of the ensuing disease they permit in response to a constant autoantigenic MOG challenge. Furthermore, the MHC haplotype determines the amount of autoantigen needed to induce disease. Thus, MHC haplotypes are not strictly disease permissive or resistant.Instead, there is a hierarchy in MHC haplotype regulation of disease, with high responder haplotypes such as RT1n and RT1h, intermediate ones such as RT1a ,RT1av1, RT1r3, and RT1r6, and low responders such as RT1u,RT1r2, RT1r4, and RT1l. Notably, no single haplotype is completely protected.An increase in numbers of IFN-g mRNA-expressing cells was recorded only in the disease-susceptible LEW.1AV1 and DA rat strains, although all four strains displayed similar increases after mitogenic stimulation with Con A. The numbers of anti-MOG Ab-secreting cells were also higher in DA rats and LEW.1AV1 rats than in PVGRT1a rats and ACI rats. The RT1av1 haplotype is permissive for induction of a MOG-specific autoimmune response in all strains, but the functional maturation of this response is strongly influenced by non-MHC genes.	This study strongly suggests that the mechanism for MHC haplotype regulation of the degree of ensuing disease is by regulation of the quantity and quality of the autoimmune response after autoantigenic challenge, since these factors directly correlated to each other.	9739061	Details
TRIM5	SNP	rs3802981	a SequenomH platform (San Diego, California) and the iPLEX gold reaction	MS	Disease risk	We conclude that HERV-Fc1 and TRIM5 play a role in the etiology of multiple sclerosis.	N/A	21311761	Details
HERV-Fc1	SNP	rs391745	a SequenomH platform (San Diego, California) and the iPLEX gold reaction	MS	Disease risk	We conclude that HERV-Fc1 and TRIM5 play a role in the etiology of multiple sclerosis.	N/A	21311761	Details
CTLA4	exon 1 dimorphism	( + 49)A/G	AD-PCR	MS	Phenotypic risk	No differences in the allelic distribution of the G49 allele between multiple sclerosis (MS) patients and the control group was found. However, the G49 allele occurred in a significant higher percentage of patients with primary progressive MS compared to patients with bout onset of disease	ysregulation of CTLA4-driven down-regulation of T-cell function due a genetic dimorphism in exon	12458055	Details
HLA-DRB1	SNP	rs3135388	Affymetrix GeneChip Mapping 250K	MS	Disease risk	The HLA-DRB1 surrogate SNP (rs3135388) was significantly associated with MS in this study	A possible explanation for this may have been the lack of power in the initial study on this smallpopulation	18401352	Details
EVI5	SNP	rs10735781	Affymetrix GeneChip Mapping 250K	MS	Disease risk	Furthermore, two SNPs, both on chromosome 1,located in the EVI5 (ecotropic viral integration site 5) gene gave significant P-values in our replication study:rs10735781 (P0.01, OR2.01, 95% CI 1.19–3.39) andrs6680578 (P0.01, OR1.9, 95% CI 1.16–3.11).	It is still not clear whether thecausal allele acts through EVI5 itself.	18401352	Details
EVI5	SNP	rs6680578	Affymetrix GeneChip Mapping 250K	MS	Disease risk	Furthermore, two SNPs, both on chromosome 1,located in the EVI5 (ecotropic viral integration site 5) gene gave significant P-values in our replication study:rs10735781 (P0.01, OR2.01, 95% CI 1.19–3.39) andrs6680578 (P0.01, OR1.9, 95% CI 1.16–3.11).	It is still not clear whether thecausal allele acts through EVI5 itself.	18401352	Details
IL7R	SNP	rs689732	Affymetrix GeneChip Mapping 250K	MS	Disease risk	The IL7RA rs689732 and for IL2RA rs12722489 and rs2104286,SNPs were not significantly associated with MS	N/A	18401352	Details
IL2RA	SNP	rs12722489	Affymetrix GeneChip Mapping 250K	MS	Disease risk	The IL7RA rs689732 and for IL2RA rs12722489 and rs2104286,SNPs were not significantly associated with MS	N/A	18401352	Details
IL2RA	SNP	rs2104286	Affymetrix GeneChip Mapping 250K	MS	Disease risk	The IL7RA rs689732 and for IL2RA rs12722489 and rs2104286,SNPs were not significantly associated with MS	N/A	18401352	Details
EVI5	SNP	rs10735781	Affymetrix GeneChip Mapping 250K	MS	Disease risk	Furthermore, two SNPs, both on chromosome 1,located in the EVI5 (ecotropic viral integration site 5) gene gave significant P-values in our replication study:rs10735781 (P0.01, OR2.01, 95% CI 1.19–3.39) andrs6680578 (P0.01, OR1.9, 95% CI 1.16–3.11).	It is still not clear whether thecausal allele acts through EVI5 itself.	18401352	Details
EVI5	SNP	rs6680578	Affymetrix GeneChip Mapping 250K	MS	Disease risk	Furthermore, two SNPs, both on chromosome 1,located in the EVI5 (ecotropic viral integration site 5) gene gave significant P-values in our replication study:rs10735781 (P0.01, OR2.01, 95% CI 1.19–3.39) andrs6680578 (P0.01, OR1.9, 95% CI 1.16–3.11).	It is still not clear whether thecausal allele acts through EVI5 itself.	18401352	Details
PCK1	SNP	rs8192708G	Affymetrix Genome-wide Human SNP Array 6.0 (Genechip 6.0)	MS、AD	Disease risk	Our study provides suggestive evidence for greater brain atrophy in MS patients bearing the PCK1 allele associated with AD-susceptibility, yielding new insights into potentially shared neurodegenerative process between MS and late onset AD	Brain atrophy and cognitive dysfunction are neurodegenerative features of Multiple Sclerosis (MS). We used a candidate gene approach to address whether genetic variants implicated in susceptibility to late onset Alzheimer’s Disease (AD) influence brain volume and cognition in MS patients	21152065	Details
PICALM	SNP	rs3851179	Affymetrix Genome-wide Human SNP Array 6.0 (Genechip 6.0)	MS、AD	Disease risk	Our study provides suggestive evidence for greater brain atrophy in MS patients bearing the PCK1 allele associated with AD-susceptibility, yielding new insights into potentially shared neurodegenerative process between MS and late onset AD	Brain atrophy and cognitive dysfunction are neurodegenerative features of Multiple Sclerosis (MS). We used a candidate gene approach to address whether genetic variants implicated in susceptibility to late onset Alzheimer’s Disease (AD) influence brain volume and cognition in MS patients	21152065	Details
CR1	SNP	rs6656401	Affymetrix Genome-wide Human SNP Array 6.0 (Genechip 6.0)	MS、AD	Disease risk	Our study provides suggestive evidence for greater brain atrophy in MS patients bearing the PCK1 allele associated with AD-susceptibility, yielding new insights into potentially shared neurodegenerative process between MS and late onset AD	Brain atrophy and cognitive dysfunction are neurodegenerative features of Multiple Sclerosis (MS). We used a candidate gene approach to address whether genetic variants implicated in susceptibility to late onset Alzheimer’s Disease (AD) influence brain volume and cognition in MS patients	21152065	Details
CLU	SNP	rs11136000	Affymetrix Genome-wide Human SNP Array 6.0 (Genechip 6.0)	MS、AD	Disease risk	Our study provides suggestive evidence for greater brain atrophy in MS patients bearing the PCK1 allele associated with AD-susceptibility, yielding new insights into potentially shared neurodegenerative process between MS and late onset AD	Brain atrophy and cognitive dysfunction are neurodegenerative features of Multiple Sclerosis (MS). We used a candidate gene approach to address whether genetic variants implicated in susceptibility to late onset Alzheimer’s Disease (AD) influence brain volume and cognition in MS patients	21152065	Details
ZNF224	SNP	rs3746319	Affymetrix Genome-wide Human SNP Array 6.0 (Genechip 6.0)	MS、AD	Disease risk	Our study provides suggestive evidence for greater brain atrophy in MS patients bearing the PCK1 allele associated with AD-susceptibility, yielding new insights into potentially shared neurodegenerative process between MS and late onset AD	Brain atrophy and cognitive dysfunction are neurodegenerative features of Multiple Sclerosis (MS). We used a candidate gene approach to address whether genetic variants implicated in susceptibility to late onset Alzheimer’s Disease (AD) influence brain volume and cognition in MS patients	21152065	Details
CCR5	deletion	N/A	agarose gel electrophoresis	MS	Disease risk	According to our study, the delta 32 allele of the CCR5 gene might be a predisposing factor for MS development in the Iranian population.	N/A	19479371	Details
TNF	polymorphism	TNFα–308	allele-specific PCR	MS	Phenotypic risk	As for the course of the disease, patients were divided into 2 groups: bout onset disease (RR and secondary progressive) and primary progressive disease.No differences were found in TNF2 allelic frequencies between the subgroups of MS patients subdivided according to the course and the familial occurrence of the disease.	TNF has been considered as the prototypic cytopathogenic cytokine in MS, due to its effects on the induction of adhesion molecules on endothelial cells and enhancement of circulating cell entry in the central nervous system (CNS) , as well as on induction of oligodendrocyte injury and demyelination.	12824709	Details
HLA-DRB1	polymorphisms	from DR1 to DR18	allele-specific PCR	MS	Disease risk	We detected a significant linkage/association between MS and the HLA -DRB1 *15.	A repeatedly confirmed fact is that particular alleles (depending on the population ethnicity) of the HLA -DRB1 gene class II are involved in the development of MS. This gene encodes the β-chain of the heterodimer, which presents the antigen to CD4+ T-lymphocytes.	22649676	Details
IFNG	SNP	874A/T	allele-specific PCR	MS	Disease risk	In the IFN-γ +874A/T gene single nucleotide polymorphism (SNP), the most allelic and genotypic frequencies in MS patients were the A allele and the AT genotype.The T allele in the IFN-γ gene (+874) was considered as potential risk factors for MS.	Cytokines are polypeptides that play critical roles in immune responses. Gene polymorphisms occurring in the inflammatory cytokines are taking a role in autoimmune diseases, including multiple sclerosis (MS), which may induce inappropriate immune responses.	32368988	Details
TNF	SNP	308A/G	allele-specific PCR	MS	Disease risk	For the TNF-α 308 G/A SNP, the highest allelic and genotypic frequencies in MS patients were the G allele and AG genotype.The genotypes of AA and AG at the TNF-α gene (-308) at the position-308 were considered as potential risk factors for MS.	Cytokines are polypeptides that play critical roles in immune responses. Gene polymorphisms occurring in the inflammatory cytokines are taking a role in autoimmune diseases, including multiple sclerosis (MS), which may induce inappropriate immune responses.	32368988	Details
CRYAB	gene Polymorphism	-C249G	allele-specific PCR approach	MS	Disease risk	Carriers of the rare allele CRYAB–650*C had an increased likelihood of a noninflammatory, neurodegenerative phenotype characterized by a relatively rapid, primary progressive clinical disease course.	nfluenced susceptibility as well as disease expression in MS	14610128	Details
CRYAB	gene Polymorphism	-C650G	allele-specific PCR approach	MS	Disease risk	Carriers of the rare allele CRYAB–650*C had an increased likelihood of a noninflammatory, neurodegenerative phenotype characterized by a relatively rapid, primary progressive clinical disease course.	nfluenced susceptibility as well as disease expression in MS	14610128	Details
CRYAB	gene Polymorphism	-A652G	allele-specific PCR approach	MS	Disease risk	Carriers of the rare allele CRYAB–650*C had an increased likelihood of a noninflammatory, neurodegenerative phenotype characterized by a relatively rapid, primary progressive clinical disease course.	nfluenced susceptibility as well as disease expression in MS	14610128	Details
TNF	polymorphism	TNF1/l ,TNF1 /2 ,TNF2/2	allelespecific PCR (ASPCR)	MS	Disease risk	No significant difference regarding the TNF alpha-308 polymorphism was observed between MS patients and controls.	Variations in the region responsible for transcriptional regulation may have implications for the levels of TNF-(r gene expression, and variability of TNF-a synthesis could be an important factor in the pathogenesis of MS .	8550811	Details
NR3C1	polymorphism	N363S, ER22/23EK, BclIG	Allelic Discrimination Assays	MS	Disease risk	For the ER22/23EK and the N363S variants no homozygous carriers were found.Genotype frequencies were not significantly different between HC and MS patients and the MS subgroups.The two other polymorphisms were not related to GC sensitivity.We defined 'real non-carriers' as having neither the N363S nor the BclIG allele.'Carriers' were cases carrying both the N363S and the BclIG allele.When only one of these polymorphisms was present, cases were defined as 'partly carriers'.In HC, 'real non-carriers' (carrying neither the N363S nor the BclIG allele) were significantly more sensitive to GC compared to 'partly carriers' .In MS patients there was no significant difference.	In several inflammatory or autoimmune diseases,evidence of decreased GC sensitivity of blood cells has been reported.Within the normal population, several polymorphisms have been described.At least three of these have been associated with altered GC sensitivity in vivo in healthy controls ,which is involved in the transactivation process.	16083972	Details
TNF	allele	–308 in the TNFα promotor	allelic discrimination PCR	MS	Disease risk	We found no statistically significant differences between the TNF2 allelic frequencies in the groups of patients with MS, ALS, and stroke.	Tumor-necrosis factor-α (TNFα) is a major proinflammatory cytokine secreted mainly by macrophages and the TH1 subset of T-helper cells. Increased expression of TNFα has been shown to be associated with clinical activity in relapsing remitting MS and the development of chronic progressive disease. TNFα augments the immune response by induction of MHC class II antigens, adhesion molecule expression, and blood-brain barrier dysfunction. Finally, TNFα has been shown directly to cause oligodendrocyte damage and demyelination in vitro.	10552245	Details
HLA-DRB1	haplotype	N/A	an allele-specific PCR amplification method	MS	Disease risk	There were no significant differences between maternal and paternal transmission of these alleles to affected and unaffected children and no transmission distortion of these alleles between mothers and fathers to sons and daughters,suggesting that noninherited resistance alleles do not appear to play a role in MS.	N/A	18433881	Details
APOE	SNP	SNP469,SNP457,SNP992,APOE,SNP952,SNP873,SNP888,SNP988	an oligonucleotide ligation assay	MS	Disease risk	Both the global and haplotype-specific multilocus results indicated that the 21112 haplotype of markers APOE, snp952, snp873, snp888, and snp988 was associated with increased MS susceptibility.APOE-4 carriers are more likely to be affected with severe disease , whereas a higher proportion of APOE-2 carriers exhibit a mild disease course .No significant effect of APOE genotypes on rate of progression to disability was detected.	One of several candidate genes in the 19q13 region is the APOE gene, which codes for a major lipid carrier protein (apoE) in the brain. The apoE protein has long been associated with regeneration of axons and myelin after lesions of central and peripheral nervous tissue, and its isoforms have been shown to have differential effects on neuronal growth.	11836653	Details
NINJ2	SNP	rs11833579	ARMS-PCR	MS	Disease risk	There were no significant difference in the alleles and genotypes frequencies of rs11833579 between cases and controls.Based on the D’ and r statistics, the mentioned SNPS were not in strong linkage disequilibrium.	Ninjurin 2 (NINJ2) participates in the process of nerve regeneration after nerve damage.As a protein which regulates the attachment of monocytes to endothelial cells and thus controls the relocation of immune cells to the CNS. Notably, based on the results of co-expression investigations, NINJ2 participates in immune system-associated pathways. Therefore, NINJ2 has prominent roles in nerve regeneration, immune response regulation and development of MS.	31292852	Details
NINJ2	SNP	rs3809263	ARMS-PCR	MS	Disease risk	The frequency of T allele of the rs3809263 was significantly higher in MS patients compared with healthy subjects.TT genotype of this SNP was associated with MS risk compared with CC genotype. Moreover, the rs3809263 was associated with MS risk in recessive model.	Ninjurin 2 (NINJ2) participates in the process of nerve regeneration after nerve damage.As a protein which regulates the attachment of monocytes to endothelial cells and thus controls the relocation of immune cells to the CNS. Notably, based on the results of co-expression investigations, NINJ2 participates in immune system-associated pathways. Therefore, NINJ2 has prominent roles in nerve regeneration, immune response regulation and development of MS.	31292852	Details
EVI5	SNP	rs6680578	ARMS-PCR	MS	N/A	The allele and genotype frequencies of rs6680578 and rs11810217 were not significantly different between cases and controls.	N/A	29141798	Details
EVI5	SNP	rs11810217	ARMS-PCR	MS	N/A	The allele and genotype frequencies of rs6680578 and rs11810217 were not significantly different between cases and controls.	N/A	29141798	Details
IL7R	SNP	rs6897932	ARMS-PCR	MS	Disease risk	Results show that rs6897932 is significantly different in and controls, while compared genotypes based on gender has shown different results.Although T/T genotype has not seen in men suffering MS, it is 4 (3.6%) in the control group.	IL7Rα functions as a receptor for two signaling cascades: IL7 and thymic stromal lymphopoietin.In the IL7 pathway, IL7 interacts with IL7Rα and the gamma chain (γc) (CD132), forming the signaling complex.The IL7/IL7RA interaction is important for the maintenance of memory T-cells and the development, proliferation, and survival of B- and T-cells, especially CD+ T-cells, which are present in inflammatory lesions of MS patients.	25422737	Details
NOS3	SNP	rs2070744	ARMS-PCR	MS	Disease risk	Statistical analysis showed that c.-813C>T polymorphism is associated with risk of MS.The prevalence of C allele was significantly higher in patients compared to the control group .	Multiple Sclerosis (MS) is a neuroimmunological disease, causing severe neurological disabilities as a result of demyelination.An important role for Nitric Oxide (NO) in the pathogenesis of MS and its influence on the various aspects of the disorder, including changes in synaptic transmission, inflammation, and neuronal death were pointed by abundant evidence.An isoform of NO producing enzymes is endothelial Nitric Oxide Synthase (NOS3) that is constitutively expressed in endothelial cells.This enzyme has been found to play a prominent role in both vasculogenesis and angiogenesis.There are two common polymorphisms of NOS3 gene in many populations that are associated with NOS3 enzyme activity and production.	29158878	Details
TNF	polymorphism	TNF-α -308	ASO-PCR	MS	Disease risk	Allelic and genotypic frequencies for this polymorphism was similar in patients with MS and population controls or among different types of the disease. The mentioned functional polymorphism is not likely to cause susceptibility to MS in the Iranian population.	Pro-inflammatory cytokines, such as tumor necrosis factor-a (TNF-a) has a detrimental role in MS induction.	17295710	Details
IRF1	allele	GT repeat alleles	automated fluorescence sequencing system	MS	Disease risk	In none of these populations, did we find any significant allelic association with disease.	Because of their complex effects on the induction and maintenance of inflammatory reactions, cytokines and interferons are considered as an important class of disease-promoting or limiting effector molecules. While administration of IFN-g leads to exacerbation of the disease, recombinant IFN-b reduces exacerbation rates and destruction of the central nervous system (CNS) components. Interferon regulatory factor-1 (IRF-1) is a transcriptional activator of the IFN-b gene, and is itself induced by cytokines such as IFN-g and IL-12.	11196707	Details
Tyk2	SNP	Tyk2rs2538-A,Tyk2rs2538-G	Bioplex multiplex cytokine assay,ELISA	EAE	Disease risk	B10.D1 mice were resistant to EAE whereas B10.Q/Ai mice were susceptible .The susceptible B10.Q/Ai mice had marked EAE pathology in the spinal cord while B10.D1 had no EAE pathology.	N/A	19494301	Details
PTPN6	methylation	N/A	bisulfite sequencing	MS	Disease risk	Over a third of MS subjects had abnormally high promoter methylation.	The protein tyrosine phosphatase, SHP-1, is a negative regulator of proinflammatory signaling and autoimmune disease. Recent evidence indicates that virus-induced DNA methylation of the SHP-1 promoter is responsible for aberrant silencing of SHP-1 expression and function in hematopoietic cells that might relate to inflammatory diseases.	22458980	Details
Foxp3	DNA methylation	N/A	bisulfite sequencing	EAE	Disease risk	T lymphocyte DNA methylation studies of the X chromosome gene Foxp3 suggested that maternal versus paternal imprinting of X chromosome genes may underlie sex differences in autoimmunity.	differential expression of the X chromosome gene Toll-like receptor 7 in neurons may contribute to sex differences in neurodegeneration.	29307297	Details
TLR3	SNP	rs3775291	capillary gel electrophoresis and TaqMan genotyping assay techniques	MS	N/A	Although the role of TLR3 and the wider toll-like receptor family remain significant in neurological and CNS inflammatory disorders, our current work does not support a role for the two tested variants in this gene with regard to MS susceptibility.	TLRs are thought to participate in modulating the Th2 (anti-inflammatory) to Th1(inflammatory) shift.	20483009	Details
TLR3	insertion-deletion TLR3 [-/A](8)	N/A	capillary gel electrophoresis and TaqMan genotyping assay techniques	MS	N/A	Although the role of TLR3 and the wider toll-like receptor family remain significant in neurological and CNS inflammatory disorders, our current work does not support a role for the two tested variants in this gene with regard to MS susceptibility.	TLRs are thought to participate in modulating the Th2 (anti-inflammatory) to Th1(inflammatory) shift.	20483009	Details
TNFSF13B	SNP	rs7318477	chip-based genotyping and next-generation sequencing	MS	Disease risk	We found that two-thirds of the tested variants (72/109) showed over representation of the Euro-pean risk allele in south Asian cases (p < 0.0003). In the rest of the Immunochip array, the most associated variant was rs7318477 which maps close to TNFSF13B, the gene for the B-cell-related protein BAFF.	In less than a decade, genomewide association studies have identified over 100 single-nucleotide variants that are associated with increased risk of developing multiple sclerosis. However, since these studies have focused almost exclusively on European populations, it is unclear what role these variants might play in determining risk in other ethnic groups.	26754803	Details
GFI1	SNP	rs11804321	Chromatin Conformation Capture (3C) assays	MS	Disease risk	In PBMCs of the risk (G) allele within SNP rs11804321, the expression of GFI1 was increased, as compared to the levels found in samples carrying the protective (A) allele either in heterozygosity or in homozygozity.	MS is a heterogeneous immunopathy likely caused by the joint participation of different peripheral blood cells in the central nervous system.Interestingly, malfunction of GFI1, which encodes a zinc-finger transcription factor, causes abnormal or malignant haematopoiesis, and therefore could play a role in an autoimmune disease such as MS.	21602820	Details
IL1A	polymorphism	IL-1 α(-889 T/C)	CTS-PCR-SSP	MS	Disease risk	Although there was no significant difference in the single allele distribution between patients and controls,genotype analysis revealed significant differences in TC and TT genotypes between these two groups .The results of our data indicate the decrease in frequency of IL-1alpha TC-889 genotype in the patients group versus normal subjects. On the other hand the frequency of IL-1alpha TT -889 genotype decreased significantly in the patients versus normal subjects.	It has been demonstrated that polymorphisms of many cytokine genes affect the transcriptional activities,resulting in individual variation in cytokine production.Individual variations in the cytokine production,might affect on many autoimmune diseases such as MS.	18322311	Details
IL1R1	polymorphism	IL-1R (pst1 1970 C/T)	CTS-PCR-SSP	MS	Disease risk	IL-1R position pst1 1970 showed significant differences between MS patients and normal control in alleles C and T allele frequency . In addition, significant differences between MS patients and normal people in CC and TC genotype were found.The results of our data indicate the decrease in frequency of IL-1R T pst1 1970 allele in the patients group versus normal subjects.On the other hand the frequency of IL-1R C pst1 1970 allele and CC genotype decreased significantly in the patients versus normal subjects.	It has been demonstrated that polymorphisms of many cytokine genes affect the transcriptional activities,resulting in individual variation in cytokine production.Individual variations in the cytokine production,might affect on many autoimmune diseases such as MS.	18322311	Details
TNF	polymorphism	TNFF-α (-308 G/A and -238G/A)	CTS-PCR-SSP	MS	Disease risk	No allele and genotype was significant in -238 position and alleles were significant in -308 position .Also in -308, significant differences were shown in GG and GA genotypes.The results of our data indicate the decrease in frequency of TNF-alpha A-308 allele and AG genotype in the patients group versus normal subjects.On the other hand the frequency of TNFalpha G -308 allele and GG genotype decreased significantly in the patients versus normal subjects.	It has been demonstrated that polymorphisms of many cytokine genes affect the transcriptional activities,resulting in individual variation in cytokine production.Individual variations in the cytokine production,might affect on many autoimmune diseases such as MS.	18322311	Details
IL1B	polymorphism	IL-1β (-511 C/T and +3962 C/T)	CTS-PCR-SSP	MS	Disease risk	Two positions including -511 in promoter and + 3962 in encoding region, were studied.Analysis on allele and genotype frequency of -511 positions revealed no significant statistical difference in patient and normal group. In +3962 position,CC and CT genotypes revealed significant differences . The results of our data indicate the decrease in frequency of IL-1beta TC +3962 genotype in the patients group versus normal subjects.	It has been demonstrated that polymorphisms of many cytokine genes affect the transcriptional activities,resulting in individual variation in cytokine production.Individual variations in the cytokine production,might affect on many autoimmune diseases such as MS.	18322311	Details
IL1RN	polymorphism	IL-1Ra (mspal 11100 T/C)	CTS-PCR-SSP	MS	Disease risk	In the IL-1R antagonist at mspal 11100 C/T position,no statistically significant differences were found in alleles between total MS patients and normal controls.However,in TC and TT genotypes, significant differences were shown .The results of our data indicate the decrease in frequency of IL-1 RA TC Mspa1 11100 genotype in the patients group versus normal subjects.	It has been demonstrated that polymorphisms of many cytokine genes affect the transcriptional activities,resulting in individual variation in cytokine production.Individual variations in the cytokine production,might affect on many autoimmune diseases such as MS.	18322311	Details
APOE	Gene polymorphisms	E4 - ε2	Datebase	MS	Disease risk	Women carriers of the E4*epsilon2 allele took longer to attain an Expanded Disability Status Scale score of 6 (p = 0.015) and had more favorable ranked severity scores than noncarriers	The interaction between gender and APOE alleles could be one factor explaining the relatively favorable outcome for women with MS	15007140	Details
APOE	Gene polymorphisms	E4 - ε3	Datebase	MS	Disease risk	There was no association in men. Alleles epsilon3 or epsilon4 and promoter polymorphisms were not associated with disease course or severity.	N/A	15007140	Details
APOE	Gene polymorphisms	E4 - ε4	Datebase	MS	Disease risk	There was no association in men. Alleles epsilon3 or epsilon4 and promoter polymorphisms were not associated with disease course or severity.	N/A	15007140	Details
LAMP2	SNP	rs1194422515; rs42895; rs41300191; rs42886	Diseases 10th Revision (World Health O, 2004) code G35 ，PLINK	MS	Disease risk	concurrent disruption of both myelination and immune systems significantly increases the risk of MS onset in women	immunity	35905688	Details
AVPR2	SNP	Affx-89,012,620; Affx89,008,152; Affx89,010,658	Diseases 10th Revision (World Health O, 2004) code G36 ，PLINK	MS	Disease risk	concurrent disruption of both myelination and immune systems significantly increases the risk of MS onset in women	immunity	35905688	Details
MTMR8	SNP	rs766668643	Diseases 10th Revision (World Health O, 2004) code G37 ，PLINK	MS	Disease risk	concurrent disruption of both myelination and immune systems significantly increases the risk of MS onset in women	immunity	35905688	Details
F8	SNP	rs369414658	Diseases 10th Revision (World Health O, 2004) code G38 ，PLINK	MS	Disease risk	concurrent disruption of both myelination and immune systems significantly increases the risk of MS onset in women	immunity	35905688	Details
PORCN	SNP	rs1556974235	Diseases 10th Revision (World Health O, 2004) code G39 ，PLINK	MS	Disease risk	concurrent disruption of both myelination and immune systems significantly increases the risk of MS onset in women	immunity	35905688	Details
ELF4	SNP	rs373568641	Diseases 10th Revision (World Health O, 2004) code G40 ，PLINK	MS	Disease risk	concurrent disruption of both myelination and immune systems significantly increases the risk of MS onset in women	immunity	35905688	Details
NSDHL	SNP	rs797045835	Diseases 10th Revision (World Health O, 2004) code G41 ，PLINK	MS	Disease risk	concurrent disruption of both myelination and immune systems significantly increases the risk of MS onset in women	myelination	35905688	Details
HS6ST2	SNP	rs950792996	Diseases 10th Revision (World Health O, 2004) code G42 ，PLINK	MS	Disease risk	concurrent disruption of both myelination and immune systems significantly increases the risk of MS onset in women	myelination	35905688	Details
RBM10	SNP	rs139585263	Diseases 10th Revision (World Health O, 2004) code G43 ，PLINK	MS	Disease risk	concurrent disruption of both myelination and immune systems significantly increases the risk of MS onset in women	myelination	35905688	Details
AR	SNP	rs367604031	Diseases 10th Revision (World Health O, 2004) code G44 ，PLINK	MS	Disease risk	concurrent disruption of both myelination and immune systems significantly increases the risk of MS onset in women	myelination	35905688	Details
TAFAZZIN	SNP	rs387907218; Affx89,017,095	Diseases 10th Revision (World Health O, 2004) code G45 ，PLINK	MS	Disease risk	concurrent disruption of both myelination and immune systems significantly increases the risk of MS onset in women	myelination	35905688	Details
RIBC1	SNP	rs782346908	Diseases 10th Revision (World Health O, 2004) code G46 ，PLINK	MS	Disease risk	concurrent disruption of both myelination and immune systems significantly increases the risk of MS onset in women	other	35905688	Details
BCOR	SNP	rs199676230	Diseases 10th Revision (World Health O, 2004) code G47 ，PLINK	MS	Disease risk	concurrent disruption of both myelination and immune systems significantly increases the risk of MS onset in women	immunity	35905688	Details
DKC1	SNP	rs121912302	Diseases 10th Revision (World Health O, 2004) code G48 ，PLINK	MS	Disease risk	concurrent disruption of both myelination and immune systems significantly increases the risk of MS onset in women	other	35905688	Details
IFNG	allele	I1(761)*CA12	DNA sequencers	MS	Disease risk	Polymorphisms of IFNG may contribute to differences in susceptibility to MS between men and women	Men carriers of I1(761)*CA13 , which is in strong linkage disequilibrium with the 30(325)*A, have increased susceptibilit	15674394	Details
APOE	SNP	N/A	either a PCR-based solid-phase minisequencing method,or a sequencing-by-synthesis method involving luminometric detection of pyrophosphate	MS	Phenotypic risk	In accordance with our previously reported preliminary results,31 however, the e3/e4 genotype was more common in severe MS than in benign MS, and severe-MS patients were more often carriers of the e4 allele than benign-MS patients.At the same time, homozygosity for e4 was more common in benign MS than severe MS.	In the central nervous system (CNS), apoE is synthesized and secreted by glial cells, particularly astrocytes;it serves as a ligand mediating the uptake of plasma lipoproteins, which are vital for membrane repair, and may have neurotrophic, anti-oxidant and immunomodulatory effects as well. The e2, e3 and e4 alleles, which in reality represent cis-positioned combinations of allelic variants at two coding region single-nucleotide polymorphisms (SNPs), encode protein isoforms, designated E2, E3 and E4, that display differential receptor-binding affinity.	11990879	Details
MIR146A	SNP	rs2910164	ELISA	MS	Disease risk	the genotype (GC+CC) of rs2910164 predicted relapse compared with the GG genotype (HR=2.09 (95% CI 1.42, 3.06), p=0.0001), as well as a near-significant (p=0.07) association with MS conversion risk	relative excess risk due to interaction	29127522	Details
Il22ra2	SNP	rs17066096	ELISA	MS	Disease risk	We show that monocytes from carriers of the risk genotype of rs17066096 express more IL-22BP in vitro and cerebrospinal fluid levels of IL-22BP correlate with MS lesion load on magnetic resonance imaging.	We confirm the pathogenicity of IL-22BP in both rat and mouse models of MS and go on to suggest a pathogenic mechanism involving lack of IL-22–mediated inhibition of T cell–derived IFN-g expression.	31292217	Details
IL22	gene polymorphism	N/A	ELISA、qPCR	MS	Disease risk	We show that (1) there is a dysregulation in the expression of IL-22 and its antagonist, IL-22BP, in MS patients, (2) IL-22 targets specifically astrocytes in the human brain, and (3) this cytokine confers an increased survival of the latter cells.	tumor necrosis factor 伪-treated astrocytes had a better long-term survival capacity upon IL-22 co-treatment	26077779	Details
CD58	SNP	rs1414273	eQTL analysis	MS	Disease risk	To conclude, our analysis suggests that SNP rs1414273 is possibly implicated in the development of MS.	We provide evidence that the SNP rs1414273 might alter Drosha cleavage activity, thereby provoking partial uncoupling of CD58 gene expression and microRNA-548ac production from the shared primary transcript in immune cells.	30730892	Details
CIITA	haplotype	168A→G	Fast Real‐Time PCR	MS	Disease risk	No independent association with MS was found for either polymorphism in the Spanish cohorts tested.However, when haplotypes were compared between patients with MS and controls, a significant difference in their overall frequency distribution was observed, evidencing a protective haplotype and a risk haplotype.The MHC2TA gene influences predisposition to MS. The -168G allele is not an aetiological variant in itself, but a genetic marker of susceptibility/protection haplotypes.	MHC class II molecules are cell‐surface glycoproteins of critical importance to the adaptive immune response, as they present peptides to antigen receptors of CD4 T cells.The class II transactivator CIITA is the key element to exquisitely control the levels of MHCII expression.MHCII molecules are critical in T cell‐dependent immunity and in inflammatory response, and they contribute to numerous diseases including MS.	17012290	Details
Tcrb	Tcrb haplotype	N/A	flow cytometric,immunizing with mouse spinal-cord homogenate	EAE	N/A	Fluorescence-activated cell sorter (FACS) analyses of lymphoid cells from the F2 mice showed that the Tcrb haplotypes did not correlate with signs of encephalomyelitis (Fig. 1 and Table 2),and therefore appeared to have no or simply a minor genetic influence on disease development.	N/A	7679665	Details
CTLA4	SNP	CT60	flow cytometry	MS	Disease risk	No significant association of these polymorphisms or respective haplotypes with MS was found.	N/A	17942509	Details
CTLA4	SNP	49A/G	flow cytometry	MS	Disease risk	No significant association of these polymorphisms or respective haplotypes with MS was found.	N/A	17942509	Details
VDR	SNP	rs731236	flow-cytometry analysis	MS	Disease risk	Results showed significant differences in MBP-stimulated intracellular-VDR-expressing total lymphocyte according to rs731236 genotype. Thus, intracellular-VDR expression was augmented in TT compared to either CC or CT cells. Notably, the VDR-total median fluorescence intensity (MFI) of rs731236 TT lymphocytes was significantly increased as well compared to the values observed in CC cells.No difference in VDR expression was observed in unstimulated cells according to rs731236 genotype.	The lack of variants in the VDRE sequence of the HLADRB115 allele led to the speculation that the augmented risk of MS seen in HLA-DRB115 carriers could be secondary to its transcription regulation through the VDR/(1,25(OH)2D) complex.	21664963	Details
IL2RA	SNP	rs7093069	Genomic DNA Extraction and SNV Analysis	MS	Disease risk	The frequency of the polymorphic T allele of rs7093069 was significantly higher (p = 0.0053) in the healthy control group compared to subjects with MS	individuals carrying the IL2RA risk alleles present a significantly increased propensity of TH (T helper) cells to develop into GM-CSF- (granulocyte-macrophage colony-stimulating factor-) producing memory TH-cells and linked this genetic risk factor with a functional feature of TH-cells in MS	33224992	Details
IL2RA	SNP	rs12722598	Genomic DNA Extraction and SNV Analysis	MS	Disease risk	The frequency of allele T was significantly higher in the control healthy group than in the group of individuals with MS	individuals carrying the IL2RA risk alleles present a significantly increased propensity of TH (T helper) cells to develop into GM-CSF- (granulocyte-macrophage colony-stimulating factor-) producing memory TH-cells and linked this genetic risk factor with a functional feature of TH-cells in MS	33224992	Details
CTLA4	SNP	rs3087243	Genomic DNA Extraction and SNV Analysis	MS	Disease risk	Of the three polymorphisms tested in the CTLA4 gene, our study showed significant differences in allele and genotype frequencies only for rs3087243.	The CTLA-4 gene has been associated with susceptibility to MS	33224992	Details
CTLA4	SNP	rs231775	Genomic DNA Extraction and SNV Analysis	MS	Disease risk	Of the three polymorphisms tested in the CTLA4 gene, our study showed significant differences in allele and genotype frequencies only for rs3087243.	The CTLA-4 gene has been associated with susceptibility to MS	33224992	Details
CTLA4	SNP	rs5742906	Genomic DNA Extraction and SNV Analysis	MS	Disease risk	Of the three polymorphisms tested in the CTLA4 gene, our study showed significant differences in allele and genotype frequencies only for rs3087243.	The CTLA-4 gene has been associated with susceptibility to MS	33224992	Details
CD40	SNP	rs1883832	Genomic DNA Extraction and SNV Analysis	MS	Disease risk	Our analysis of the rs1883832 polymorphisms in the CD40 gene did not show any significant differences in the homozygous genotypes and allele frequencies between the studied groups	N/A	33224992	Details
PADI4	SNP	rs1748033	Genomic DNA Extraction and SNV Analysis	MS	Disease risk	We did not observe any significant differences between the studied groups in the frequencies of alleles and the genotypes of rs1748033 in the PADI4 gene	N/A	33224992	Details
PLCG2	SNP	rs72824905	GWAS	MS	Disease risk	Importantly, rs72824905 G allele could also significantly reduce the risk of MS with OR = 0.94, p = 3.63E-05. Hence, the effects of rs72824905 on AD and MS are consistent.	N/A	33523007	Details
Icam1	Differential Isoform Expression	N/A	hematoxylin and eosin	EAE	Disease risk	the alternatively spliced ICAM-1 isoforms are functional, and play key roles during the progression of CNS inflammation and demyelination in EAE	with ICAM-1 ligands such as Mac-1.	20371120	Details
IL2RA	SNP	rs12722489	high multiplexed iPlexes	MS	Disease risk	The SNP rs12722489, also located within the IL2RA gene, shows significant association in the German sample and a positive trend in the French trios.	Variations in the interleukin-2 receptor-a gene (IL2RA) were demonstrated to confer a risk for MS in candidate gene approaches and a whole genome screen.	18354419	Details
IL2RA	SNP	rs2104286	high multiplexed iPlexes	MS	Disease risk	The SNP rs2104286 within the IL2RA gene demonstrated a significant association in the French MS trios and the German sample—whether analysed separately or combined in both samples.	Variations in the interleukin-2 receptor-a gene (IL2RA) were demonstrated to confer a risk for MS in candidate gene approaches and a whole genome screen.	18354419	Details
IL7R	SNP	rs6897932	high multiplexed iPlexes	MS	Disease risk	The SNP rs6897932 located within the IL7RA gene exhibits a significant association in the French trios and a positive trend in the German sample.	Variations in the interleukin-7 receptor-a chain (IL7RA) were demonstrated to confer a risk for MS in candidate gene approaches and a whole genome screen.	18354419	Details
APOE	Alleles	ε4、ε3/ε4	Hixon and Vernier	MS	Disease risk	Comparison between carriers of at least one ε4 allele to the remainder of the study population confirmed a trend towards a higher T2-LL (15.1 (SD 13.7) v 10.4 (SD 9.2) cm3, p=0.24) and a significantly greater T1-LL (2.4 (SD 3.2) v 1.3 (SD 2.8) cm3, p=0.044) and black hole ratio (13.3 (SD 11.8)v 8.3 (SD 12.5)%, p=0.024) in ε4 patients (figure A–C).	which can be attributed to more extensive tissue destruction or less efficient repair in carriers of the ε4 allele	10864599	Details
APOE	Alleles	ε2/ε3	Hixon and Vernier	MS	Disease risk	Comparison between carriers of at least one ε4 allele to the remainder of the study population confirmed a trend towards a higher T2-LL (15.1 (SD 13.7) v 10.4 (SD 9.2) cm3, p=0.24) and a significantly greater T1-LL (2.4 (SD 3.2) v 1.3 (SD 2.8) cm3, p=0.044) and black hole ratio (13.3 (SD 11.8)v 8.3 (SD 12.5)%, p=0.024) in ε4 patients (figure A–C).	N/A	10864599	Details
APOE	Alleles	ε3/ε3	Hixon and Vernier	MS	Disease risk	Comparison between carriers of at least one ε4 allele to the remainder of the study population confirmed a trend towards a higher T2-LL (15.1 (SD 13.7) v 10.4 (SD 9.2) cm3, p=0.24) and a significantly greater T1-LL (2.4 (SD 3.2) v 1.3 (SD 2.8) cm3, p=0.044) and black hole ratio (13.3 (SD 11.8)v 8.3 (SD 12.5)%, p=0.024) in ε4 patients (figure A–C).	N/A	10864599	Details
CD58	SNP	rs12044852	hME SNP typing facility	MS	Disease risk	The case– control analysis indicates that risk alleles associated with the CD58 genes are overrepresented in familial MS cases as compared with disease-free control subjects .	N/A	19506219	Details
IL7R	SNP	rs6897932	hME SNP typing facility	MS	Disease risk	The case– control analysis indicates that risk alleles associated with the IL7R genes are overrepresented in familial MS cases as compared with disease-free control subjects .	N/A	19506219	Details
CLEC16A	SNP	rs6498169	hME SNP typing facility	MS	Disease risk	The case– control analysis indicates that risk alleles associated with the KIAA0350 genes are overrepresented in familial MS cases as compared with disease-free control subjects .	N/A	19506219	Details
IL2RA	SNP	rs12722489	hME SNP typing facility	MS	Disease risk	The case– control analysis indicates that risk alleles associated with the IL2RA genes are overrepresented in familial MS cases as compared with disease-free control subjects .	N/A	19506219	Details
IL2RA	SNP	rs2104286	hME SNP typing facility	MS	Disease risk	The case– control analysis indicates that risk alleles associated with the IL2RA genes are overrepresented in familial MS cases as compared with disease-free control subjects .	N/A	19506219	Details
CBLB	SNP	rs12487066	hME SNP typing facility	MS	Disease risk	The case– control analysis indicates that risk alleles associated with the CBLB genes are overrepresented in familial MS cases as compared with disease-free control subjects .	N/A	19506219	Details
C3	polymorphism	N/A	horizontal high voltage agarose gel electrophoresis	MS	Disease risk	A significantly increased frequency of the C3F-gene was found among the patients, and closely associated with the occurrence of CIC.	A possible explanation involves the hypothesis, that the patients with low C3 levels, but without detectable CIC, could suffer from a type 11 reaction disease.	7211174	Details
AIRE	SNP	rs1800520	HRM real-time PCR	MS	Disease risk	Results showed that AIRE SNP rs1800520 was significantly less common in the MS patients than in healthy controls. Also, the frequency of allele G was significantly higher among the control group than in the case group.	The co-occurrence of autoimmune diseases in the same individual has prompted several studies aimed to recognize shared pathophysiological mechanisms. AIRE protein acts as a powerful transcriptional trans-activator. The highest level of AIRE expression is in thymus where it is seen in a subpopulation of modularly Thymic Epithelial Cells (mTEC).In mTECs, AIRE is required for the expression of many Tissue-Restricted self-Antigens (TRAs).The expression of TRAs in mTECs allows the negative selection of autoreactive lymphocytes.In the absence of functional AIRE, human patients and mice develop multi-organ autoimmune disease due to a defect in thymic negative selection.	29849988	Details
HTR2A	DNA methylation	N/A	Illumina 450K/EPIC arrays,ChAMP	MS	Disease risk	HTR2A is differentially methylated in progressive MS independent of genotype. This differential methylation is not evident in RRMS, making it a potential biomarker of progressive disease.	N/A	33335118	Details
HLA-DRB1	genotype	DRB1*15	Illumina 660-Quad platform	MS	Phenotypic risk	Our results confirm that HLA DRB1*15 is positively associated with OCB+.	N/A	23785401	Details
IFNLR1	SNP	rs4649203	Illumina Bead Array Matrix SNP panel	MS	Disease risk	We did not detect any consistent association of this locus with MS after an exhaustive investigation of polymorphisms.	IL28RA codes for a transmembrane protein that heterodimerizes with another subunit, IL-10RB, to form a type II cytokine receptor, which binds IL-28A, IL-28B and IL-29. These ligands, which are distantly related to class I interferons, are activated upon viral infection and trigger the JAK-STAT signaling pathway to exert antiviral activity. The class III interferon pathway is likely to influence susceptibility to various inflammatory and infectious diseases, and polymorphisms in genes integrating this pathway have been related to several conditions.	22386267	Details
SLFN12	methylation	N/A	Illumina BeadChips	MS	Disease risk	A long DMR covering the first exon of SLFN12 showed hypermethylation in MS patients compared to healthy controls in both CD4+ and CD8+ T cells. Hypermethylation was seen in all strata, regardless of treatment status of cases.	SLFN12 encodes a member of the Schlafen protein family, which is a family of proteins encoded by a cluster of five genes on chromosome 17.Type I IFNs induce the expression of Schlafen genes.SLFN12 has been shown to be downregulated during T-cell activation in primary human cells. From clinical observations and genetic studies,there is convincing evidence that MS pathology is driven by T-cells, and IFN beta type I is an approved therapy for MS, making SLFN12 a biologically plausible gene of interest for MS.	30379917	Details
HLA-DRB1	DRB1*15:01 allele	N/A	Illumina exome chip	MS	Disease risk	The effect of each DRB1*15:01 allele on MS risk was additive on the log-odds scale for each additional allele. Interaction between DRB1*15:01 and each assessed environmental factor was of similar magnitude regardless of the number of DRB1*15:01 alleles, although ORs were affected. When any of the environmental factors were present in DRB1*15:01 carriers without the protective A*02:01 allele, a three-way interaction occurred and rendered high ORs, especially among DRB1*15:01 homozygotes (OR 20.0, 95% CI 13.1 to 30.5 among smokers, OR 21.9, 95% CI 15.0 to 31.8 among those with elevated EBNA-1 antibody levels, and OR 44.3, 95% CI 13.5 to 145 among those who reported adolescent overweight/obesity).	HLA molecules are also involved in regulating thymic selection of the mature T-cell repertoire. By central tolerance mechanisms, potentially autoaggressive T cells with a propensity to recognise CNS autoantigens may to a higher degree survive in DRB1*15:01 positive subjects.	33687974	Details
IL2RA	methylation	N/A	Illumina HumanMethylation 450k DNA Methylation Chip	MS	Disease risk	DNA methylation of IL2RA is decreased in T cells of MS patients compared with healthy controls.The degree of hypomethylation was differential between cases and controls at cg26316423, being more overt in those with MS.	Genetic studies have demonstrated association between single-nucleotide polymorphisms within the IL2RA (interleukin-2 receptor α-subunit) gene and risk of developing multiple sclerosis (MS).	28077880	Details
WT1	SNP	rs10767935	Illumina HumanOmniExpress12v1_A array,ANZgene MS GWAS	MS	Disease risk	We have demonstrated that two-independent SNPs (rs10767935 and rs5030244) in WT1 modified the IFN-β-25(OH)D association in patients with MS.	These findings indicate that WT1 variants may play a role in altering the effects of IFN-β on vitamin D in MS.	25312909	Details
WT1	SNP	rs5030244	Illumina HumanOmniExpress12v1_A array,ANZgene MS GWAS	MS	Disease risk	We have demonstrated that two-independent SNPs (rs10767935 and rs5030244) in WT1 modified the IFN-β-25(OH)D association in patients with MS.	These findings indicate that WT1 variants may play a role in altering the effects of IFN-β on vitamin D in MS.	25312909	Details
HLA-C	SNP	HLA-DQB1*06:02、rs9273342	Illumina Infinium custom genotyping array	MS	Disease risk	HLA-DQB1*06:02 indicated the strongest additive association with MS risk in Hispanics	MHC is vital to proper immune system function due to its central role in the initiation of adaptive immune response	36548255	Details
HLA-C	SNP	HLA-A*2:01、rs28844821	Illumina Infinium custom genotyping array	MS	Disease risk	HLA-DQB1*06:02 dominant, risk; HLA-A*2:01 additive, protective; HLA-DPB1*03:01 additive, risk; HLA-DRB1*13:03:01 additive, risk; HLA-DQB1*02:01 additive, risk; HLA-DRB1*15:01 additive, risk	MHC is vital to proper immune system function due to its central role in the initiation of adaptive immune response	36548255	Details
HLA-C	SNP	HLA-DPB1*03:01、DPB1-2939-33046757-intron1	Illumina Infinium custom genotyping array	MS	Disease risk	HLA-DQB1*06:02 dominant, risk; HLA-A*2:01 additive, protective; HLA-DPB1*03:01 additive, risk; HLA-DRB1*13:03:01 additive, risk; HLA-DQB1*02:01 additive, risk; HLA-DRB1*15:01 additive, risk	MHC is vital to proper immune system function due to its central role in the initiation of adaptive immune response	36548255	Details
HLA-C	SNP	HLA-DRB1*13:03:01、rs75589097	Illumina Infinium custom genotyping array	MS	Disease risk	HLA-DQB1*06:02 dominant, risk; HLA-A*2:01 additive, protective; HLA-DPB1*03:01 additive, risk; HLA-DRB1*13:03:01 additive, risk; HLA-DQB1*02:01 additive, risk; HLA-DRB1*15:01 additive, risk	MHC is vital to proper immune system function due to its central role in the initiation of adaptive immune response	36548255	Details
HLA-C	SNP	HLA-DQB1*02:01、DQB1-6203-32628182-intron 5	Illumina Infinium custom genotyping array	MS	Disease risk	HLA-DQB1*06:02 dominant, risk; HLA-A*2:01 additive, protective; HLA-DPB1*03:01 additive, risk; HLA-DRB1*13:03:01 additive, risk; HLA-DQB1*02:01 additive, risk; HLA-DRB1*15:01 additive, risk	MHC is vital to proper immune system function due to its central role in the initiation of adaptive immune response	36548255	Details
HLA-C	SNP	HLA-DRB1*15:01、rs9269243	Illumina Infinium custom genotyping array	MS	Disease risk	HLA-DQB1*06:02 dominant, risk; HLA-A*2:01 additive, protective; HLA-DPB1*03:01 additive, risk; HLA-DRB1*13:03:01 additive, risk; HLA-DQB1*02:01 additive, risk; HLA-DRB1*15:01 additive, risk	MHC is vital to proper immune system function due to its central role in the initiation of adaptive immune response	36548255	Details
HLA-C	SNP	r6929950	Illumina Infinium custom genotyping array	MS	Disease risk	We identified three novel protective variants for MS across the extended MHC, one in the Hispanic sample (rs6929950, an intronic variant within OR5V1) and two in the African American sample (classical HLA-B*53:01 and rs760145, an intronic variant within HLA-F-AS1)	MHC is vital to proper immune system function due to its central role in the initiation of adaptive immune response	36548255	Details
HLA-C	SNP	HLA-DRB1*15:01、rs9269243	Illumina Infinium custom genotyping array	MS	Disease risk	while HLA-DRB1*15:01 indicated the strongest additive association with MS risk in African Americans	MHC is vital to proper immune system function due to its central role in the initiation of adaptive immune response	36548255	Details
HLA-C	SNP	HLA-A*02:01、rs12153924	Illumina Infinium custom genotyping array	MS	Disease risk	HLA-DRB1*15:01 dominant, risk; HLA-A*02:01 additive, protective; HLA-B*53:01 dominant, protective	MHC is vital to proper immune system function due to its central role in the initiation of adaptive immune response	36548255	Details
HLA-C	SNP	HLA-B*53:01、rs115219755	Illumina Infinium custom genotyping array	MS	Disease risk	HLA-DRB1*15:01 dominant, risk; HLA-A*02:01 additive, protective; HLA-B*53:01 dominant, protective	MHC is vital to proper immune system function due to its central role in the initiation of adaptive immune response	36548255	Details
HLA-C	SNP	rs760145	Illumina Infinium custom genotyping array	MS	Disease risk	We identified three novel protective variants for MS across the extended MHC, one in the Hispanic sample (rs6929950, an intronic variant within OR5V1) and two in the African American sample (classical HLA-B*53:01 and rs760145, an intronic variant within HLA-F-AS1)	MHC is vital to proper immune system function due to its central role in the initiation of adaptive immune response	36548255	Details
Tagap	Deletion	N/A	immunoblot analysis,co-immunoprecipitation	heat-killed C. albicans, Curdlan, and α-Mannan infection	Disease risk	TAGAP can bind Dectin-1, whereas TAGAPΔGAP cannot. TAGAP also bound to Dectin-2, whereas TAGAPΔGAP did not.Wild-type TAGAP interacted with EPHB2 whereas TAGAPΔGAP mutant showed greatly reduced binding to EPHB2.	The GAP domain of TAGAP is essential for the recruitment of TAGAP to Dectin-1 and mediating the binding to EPHB2.	32312989	Details
HLA-DRB1	allele	DRB1*15	Infinium 660K BeadChip or HumanOmniExpress BeadChip	POMS	Disease risk	Without high ozone exposure, the presence of HLA-DRB1*15 alleles did not significantly increase the odds of POMS.When both HLA-DRB1*15 alleles and high ozone exposure were present, the odds of having POMS increased to 3.89.	N/A	35000467	Details
CD86	SNP	rs928264	Infinium 660K BeadChip or HumanOmniExpress BeadChip	POMS	Disease risk	Without high ozone exposure, the presence of the GG genotype of CD86 SNP did not significantly increase the odds of having POMS.Conversely, without the GG genotype of CD86 SNP, high ozone exposure was not associated with increased odds of POMS.When both GG genotype of CD86 SNP and high ozone exposure were present, the odds ratio of POMS increased to 4.06.	N/A	35000467	Details
AHI1	SNP	rs11154801	Infinium 660K BeadChip,HumanOmniExpress BeadChip	MS	Disease risk	After adjustment for genetic ancestry, sex, age, vitamin D level, DMT use and HLA-DRB1*15 status, having two copies of the MS risk allele within AHI1 (rs11154801) was associated with increased relapses among children (HR = 1.75,95%CI = 1.18-2.48, p = 0.006) and this result was also observed among adults (HR = 1.81,95%CI = 1.05-3.03, p = 0.026).	Our results suggest that the MS genetic risk variant within the gene AHI1 may contribute to disease course in addition to disease susceptibility.	29409597	Details
H2	N/A	N/A	injected monitored for clinical GVHD ,flow cytometry staining	EAE	Disease risk	Induction of mixed chimerism prevents EAE relapse, augments myelin sheath regeneration, prevents axon damage,reverses autoimmunity and eliminates lymphocyte infiltration in spinal tissue,reduces Th17 and increases host-type Treg as well as increases thymic Treg production.Induction of mixed chimerism in thymectomized recipients does not prevent EAE relapse but reduces its severity. Induction of mixed chimerism in late-stage EAE mice eliminates infiltration in spinal tissues but does not cure disease.	The mechanisms behind this observation remain unclear and may be explained by the following hypothesis: Although H-2s SJL/J mice are susceptible to induction of EAE by antigen stimulation, the mice never spontaneously develop autoimmune EAE. This phenomenon suggests that under the normal situation, the autoreactive T cells in the peripheral lymphoid tissues of SJL/J mice are tolerized, probably by regulatory T cells such as Foxp3+ Treg cells. After induction of EAE, peripheral autoreactive CD4+ T cells are expanded, infiltrate the CNS, and cause damage of myelin sheaths, axons, and eventually neurons. At the same time, autoreactive T cells migrate into the thymus to damage medullary thymic epithelial cells (mTEC) and impair negative selection. Subsequently, more autoreactive T cells are generated and the disease is perpetuated. Autoreactive T cells can have dual TCRs and have cross-reactivity with mismatched MHC .	26647186	Details
ASAP2	SNP	rs1109670	iPLEX Sequenom MassARRAY ,PicoGreen	MS	Disease risk	Only rs9523762 mapping in the GPC5gene was significantly associated(G allele, P1.6 10 5 ; odds ratio (95% confidence interval)1.23 (1.12–1.36)), supporting a role for this proteoglycan in MS predisposition	MS predisposition	20944657	Details
PDZRN4	SNP	rs1458175	iPLEX Sequenom MassARRAY ,PicoGreen	MS	Disease risk	Only rs9523762 mapping in the GPC5gene was significantly associated(G allele, P1.6 10 5 ; odds ratio (95% confidence interval)1.23 (1.12–1.37)), supporting a role for this proteoglycan in MS predisposition	MS predisposition	20944657	Details
CSMD1	SNP	rs1529316	iPLEX Sequenom MassARRAY ,PicoGreen	MS	Disease risk	Only rs9523762 mapping in the GPC5gene was significantly associated(G allele, P1.6 10 5 ; odds ratio (95% confidence interval)1.23 (1.12–1.38)), supporting a role for this proteoglycan in MS predisposition	MS predisposition	20944657	Details
CSMD1	SNP	rs2049306	iPLEX Sequenom MassARRAY ,PicoGreen	MS	Disease risk	Only rs9523762 mapping in the GPC5gene was significantly associated(G allele, P1.6 10 5 ; odds ratio (95% confidence interval)1.23 (1.12–1.39)), supporting a role for this proteoglycan in MS predisposition	MS predisposition	20944657	Details
TBC1D2	SNP	rs16914086	iPLEX Sequenom MassARRAY ,PicoGreen	MS	Disease risk	Only rs9523762 mapping in the GPC5gene was significantly associated(G allele, P1.6 10 5 ; odds ratio (95% confidence interval)1.23 (1.12–1.40)), supporting a role for this proteoglycan in MS predisposition	MS predisposition	20944657	Details
SH3GL2	SNP	rs1755289	iPLEX Sequenom MassARRAY ,PicoGreen	MS	Disease risk	Only rs9523762 mapping in the GPC5gene was significantly associated(G allele, P1.6 10 5 ; odds ratio (95% confidence interval)1.23 (1.12–1.41)), supporting a role for this proteoglycan in MS predisposition	MS predisposition	20944657	Details
ZIC1	SNP	rs1841770	iPLEX Sequenom MassARRAY ,PicoGreen	MS	Disease risk	Only rs9523762 mapping in the GPC5gene was significantly associated(G allele, P1.6 10 5 ; odds ratio (95% confidence interval)1.23 (1.12–1.42)), supporting a role for this proteoglycan in MS predisposition	MS predisposition	20944657	Details
EN1	SNP	rs651477	iPLEX Sequenom MassARRAY ,PicoGreen	MS	Disease risk	Only rs9523762 mapping in the GPC5gene was significantly associated(G allele, P1.6 10 5 ; odds ratio (95% confidence interval)1.23 (1.12–1.43)), supporting a role for this proteoglycan in MS predisposition	MS predisposition	20944657	Details
TRIB2	SNP	rs7607490	iPLEX Sequenom MassARRAY ,PicoGreen	MS	Disease risk	Only rs9523762 mapping in the GPC5gene was significantly associated(G allele, P1.6 10 5 ; odds ratio (95% confidence interval)1.23 (1.12–1.44)), supporting a role for this proteoglycan in MS predisposition	MS predisposition	20944657	Details
TMEM74B	SNP	rs397020	iPLEX Sequenom MassARRAY ,PicoGreen	MS	Disease risk	Only rs9523762 mapping in the GPC5gene was significantly associated(G allele, P1.6 10 5 ; odds ratio (95% confidence interval)1.23 (1.12–1.45)), supporting a role for this proteoglycan in MS predisposition	MS predisposition	20944657	Details
SLC25A36	SNP	rs908821	iPLEX Sequenom MassARRAY ,PicoGreen	MS	Disease risk	Only rs9523762 mapping in the GPC5gene was significantly associated(G allele, P1.6 10 5 ; odds ratio (95% confidence interval)1.23 (1.12–1.46)), supporting a role for this proteoglycan in MS predisposition	MS predisposition	20944657	Details
TENM3-AS1	SNP	rs7672826	iPLEX Sequenom MassARRAY ,PicoGreen	MS	Disease risk	Only rs9523762 mapping in the GPC5gene was significantly associated(G allele, P1.6 10 5 ; odds ratio (95% confidence interval)1.23 (1.12–1.47)), supporting a role for this proteoglycan in MS predisposition	MS predisposition	20944657	Details
GPC5	SNP	rs9523762	iPLEX Sequenom MassARRAY ,PicoGreen	MS	Disease risk	Only rs9523762 mapping in the GPC5gene was significantly associated(G allele, P1.6 10 5 ; odds ratio (95% confidence interval)1.23 (1.12–1.48)), supporting a role for this proteoglycan in MS predisposition	MS predisposition	20944657	Details
HLA-DRB1	SNP	rs3135388	iPlex SNP assay design system	MS	Disease risk	We observed a trend for association of rs3135388 (HLA-DRB1*1501)with a younger age at MS onset and have remained significant when being over conservative and adjusting for multiple testing.	N/A	22411505	Details
DIPK1A	SNP	rs7536563	iPlex SNP assay design system	MS	Disease risk	have remained significant when being over conservative and adjusting for multiple testing	N/A	22411505	Details
CLEC16A	SNP	rs725613, rs12708716	iPlex SNP assay design system	MS	Disease risk	have remained significant when being over conservative and adjusting for multiple testing	N/A	22411505	Details
IL7R	SNP	rs6897932	iPlex SNP assay design system	MS	Disease risk	The additional non-MHC loci showing association without adjusting for multiple testing.	N/A	22411505	Details
IL2RA	SNP	rs2104286, rs35285258	iPlex SNP assay design system	MS	Disease risk	We observed a trend for association of rs7090530 (IL2RA) with a younger age at MS onset.The additional non-MHC loci showing association without adjusting for multiple testing.	N/A	22411505	Details
RPL5	SNP	rs10735781 rs6680578 rs6604026	iPlex SNP assay design system	MS	Disease risk	The additional non-MHC loci showing association without adjusting for multiple testing.	N/A	22411505	Details
KANK1	SNP	rs10975200	iPlex SNP assay design system	MS	Disease risk	The opposite A allele was associated with the risk of MS in our population.The additional non-MHC loci showing association without adjusting for multiple testing.	N/A	22411505	Details
MBOAT2	SNP	rs11109670	iPlex SNP assay design system	MS	Disease risk	The additional non-MHC loci showing association without adjusting for multiple testing.	N/A	22411505	Details
TBC1D2	SNP	rs16914086	iPlex SNP assay design system	MS	Disease risk	The additional non-MHC loci showing association without adjusting for multiple testing.	N/A	22411505	Details
IL1B	SNP	-500 C/T ï¼›rs16944	IPLEXTM on SEQUENOM MASSARRAY	MS	Disease risk	Our findings support the existence of a causative variant for MS within this candidate region in a representative Italian Caucasian population and, in particular, the role of the IL-1 beta ()511 C/T) variant warrants further investigation.	causative variant	20192980	Details
IL1B	SNP	+3954 C/T ;rs1143634	IPLEXTM on SEQUENOM MASSARRAY	MS	Disease risk	Our findings support the existence of a causative variant for MS within this candidate region in a representative Italian Caucasian population and, in particular, the role of the IL-1 beta ()512 C/T) variant warrants further investigation.	causative variant	20192980	Details
IL1A	SNP	-889 C/T; rs1800587	IPLEXTM on SEQUENOM MASSARRAY	MS	Disease risk	Our findings support the existence of a causative variant for MS within this candidate region in a representative Italian Caucasian population and, in particular, the role of the IL-1 beta ()513 C/T) variant warrants further investigation.	causative variant	20192980	Details
IL1A	SNP	+4845 G/T; rs17561	IPLEXTM on SEQUENOM MASSARRAY	MS	Disease risk	Our findings support the existence of a causative variant for MS within this candidate region in a representative Italian Caucasian population and, in particular, the role of the IL-1 beta ()514 C/T) variant warrants further investigation.	causative variant	20192980	Details
Vav1	polymorphism	Vav1R63W	knock-in	EAE	Disease risk	Vav1R63W mice display reduced susceptibility to experimental autoimmune encephalomyelitis (EAE) induced by MOG35-55 peptide immunization.Although the incidence of the disease was similar between the two groups, Vav1R63W mice developed a less severe disease, with delayed onset and quicker recovery resulting in reduced clinical scores .However, the CNS-infiltrating CD4 T cells from both the brain and spinal cord of MOG35-55-immunized Vav1R63W mice produced significantly less IFN-γ, IL-17 and GM-CSF.	The guanine nucleotide exchange factor (GEF) Vav1 is essential for transducing T cell antigen receptor (TCR) signals and therefore plays a critical role in the development and activation of T cells.A recent study has shown that many critical events involved in T cell activation are mediated by either the GEF or the scaffolding activities of Vav1.The GEF activity of Vav1 is necessary for T cell development and for the optimal activation of T cells, including signal transduction to Rac1, Akt, and integrins.	27438086	Details
KIR3DL1	SNP	N/A	LABType	MS	Disease risk	The protective effect was observed only in individuals who were not positive for the MS risk allele HLA-DRB1*15:01	The observed effect cannot be explained by either a specific HLA-B allele or by linkage disequilibrium with HLA-DRB1 or HLA-A.	26866467	Details
HLA-B	SNP	HLA-Bw4	LABType	MS	Disease risk	The protective effect was observed only in individuals who were not positive for the MS risk allele HLA-DRB1*15:01	The observed effect cannot be explained by either a specific HLA-B allele or by linkage disequilibrium with HLA-DRB1 or HLA-A.	26866467	Details
MOG	Gene polymorphisms	N/A	long-range PCR	MS	Disease risk	the polymorphisms observed do not provide evidence to support a significant role for MOG in multiple sclerosis susceptibility	N/A	12149493	Details
CD58	SNP	rs1335532	Luciferase reporter constructs	MS	Disease risk	CD58 enhancer 2 containing SNP rs1335532 demonstrated 2-fold up-regulating effect on CD58 promoter activity	The minor rs1335532 allelic variant is associated with elevated CD58 promoter activity in lymphoblastic cell lines upon Wnt/β-catenin signaling pathway activation	3006149	Details
CD58	SNP	rs2300747	Luciferase reporter constructs	MS	Disease risk	CD58 enhancer 1 region containing rs2300747 did not influence CD58 promoter activity, which indicates the absence of its enhancer function	N/A	3006149	Details
HFE	polymorphisms	C282Y	meta-analysis	MS	Disease risk	The results of the meta-analysis did not show a significant association between HFE polymorphisms and susceptibility to MS in any of the genetic comparison models .	A growing body of evidence supports a possible role of iron metabolism in a number of diseases with a neurodegenerative component, including MS.A recent study in MS patients found an association between the serum iron concentration and evidence of increased iron deposition in deep gray matter subcortical structures.The human hemochromatosis gene (HFE) is an important regulator of cellular iron homeostasis and has the highest prevalence of polymorphisms amongst the iron regulatory genes known to alter brain iron levels and structure.In HFE, the single nucleotide polymorphisms C282Y and H63D can result in phenotypes with altered iron parameters.Homozygosity or compound heterozygosity for the C282Y and H63D variants can lead to iron overload and the disorder known as hereditary hemochromatosis.	34987796	Details
HFE	polymorphisms	H63D	meta-analysis	MS	Disease risk	The results of the meta-analysis did not show a significant association between HFE polymorphisms and susceptibility to MS in any of the genetic comparison models .	A growing body of evidence supports a possible role of iron metabolism in a number of diseases with a neurodegenerative component, including MS.A recent study in MS patients found an association between the serum iron concentration and evidence of increased iron deposition in deep gray matter subcortical structures.The human hemochromatosis gene (HFE) is an important regulator of cellular iron homeostasis and has the highest prevalence of polymorphisms amongst the iron regulatory genes known to alter brain iron levels and structure.In HFE, the single nucleotide polymorphisms C282Y and H63D can result in phenotypes with altered iron parameters.Homozygosity or compound heterozygosity for the C282Y and H63D variants can lead to iron overload and the disorder known as hereditary hemochromatosis.	34987796	Details
FOXP3	N/A	N/A	methylation-specific polymerase chain reaction	MS、primary immune thrombocytopenia	Disease risk	We have demonstrated that a dichotomic tTreg subset with both immunoregulatory and Th17 phenotypes is increased in the circulation of SLE patients. This tTreg subset might be involved in the pathogenic process of SLE by infiltrating into the effected tissue, although whether this subset is harmful or protective remains unclear. Further studies investigating the roles of this tTreg subset in the pathogenic process of SLE and the mechanisms underlying its differentiation are useful for understanding the pathogenesis of SLE and developing potential biomarkers and therapeutic targets	A unique tTreg subset with dichotomic immunoregulatory and T helper 17 phenotypes is increased in the circulation of SLE patients and may be involved in the pathogenic process of SLE	32317002	Details
MMP9	polymorphism	N/A	microsatellite fragment analysis	MS	Disease risk	No significant differences in overall allelic or genotype frequencies were observed between the diseased and control subpopulation.	Based on mononuclear cell infiltrations in multiple sclerosis (MS) lesions, MS is classified as an auto immune demyelinating disease of unknown etiology. The evidences for a pathophysiological role of gelatinase B in MS are multiple but circumstantial: production by mononuclear cells, detection in the cerebrospinal fluid of MS patients, but not in neurological controls, and correlation with the IgG index in MS patients, occurrence of protein and mRNA in demyelinating areas in CNS tissues of MS patients, association of immunoreactivity with lesion evolution, and parallelism of the protease load, i.e. a tendency for increased gelatinase B and decreased TIMP serum levels, with MRI analysis.	10713364	Details
NOS2	SNP	two promoter region microsatellites, (CCTTT)n and (TAAA)n, the original exon 10 C/T SNP, and an additional SNP within exon16, C/T (S569L)	microsatellite markers	MS	Disease risk	Significant PDT results were maintained for the NOS2A exon 10 C/T SNP in single-case families only and were strongest in HLA-DR2–positive families .Although there was no evidence for association with any chromosome 17q11 markers or haplotypes in the multicase families modest evidence for linkage was observed for the NOS2A (CCTTT)n promoter polymorphism and was also restricted to families in which all patients carried at least one HLA-DR2 allele.Associations between the NOS2A polymorphisms were evaluated in a sample of 232 unrelated white controls.There was significant evidence for strong LD between each pair of the (CCTTT)n, (TAAA)n, exon 10 C/T (D346D), and exon 16 C/T (S569L) polymorphisms within NOS2A.	The NOS2A locus encodes one of the three isoforms of nitric oxide (NO) synthase, inducible NOS2 oriNOS, and is a very plausible MS candidate gene based on the well-known biological functions attributed to this enzyme.	15174013	Details
VDR	polymorphisms	N/A	microsatellite markers	MS	Disease risk	At the VDR locus, TDT analysis of the ApaI and TaqI polymorphisms did not show preferential transmission of any allele to affected offspring .	A high prevalence of vitamin D deficiency has been demonstrated in MS patients.VDR is involved in the metabolism and function of vitamin D.	10680811	Details
DBP	polymorphisms	N/A	microsatellite markers	MS	Disease risk	Within the DBP gene, TDT analysis of the HaeIII and StyI genotypes showed no preferential transmission of any allele to affected offspring.	A high prevalence of vitamin D deficiency has been demonstrated in MS patients.DBP is involved in the metabolism and function of vitamin D.	10680811	Details
CYP27A1	polymorphisms	N/A	microsatellite markers	MS	Disease risk	At the 1a hydroxylase locus, three nearby microsatellite markers (D12S90, D12S355, and D12S83) were analyzed. A TDT analysis of the four most common alleles for each marker showed a slight difference in transmission for allele 10 of marker D12S355. All other alleles for D12S355 and all alleles of markers D12S85, D12S90, and D12S83 showed no deviation in transmission. We found no evidence for linkage or association of this gene with MS in the Canadian population.	A high prevalence of vitamin D deficiency has been demonstrated in MS patients.This gene is involved in the metabolism and function of vitamin D.	10680811	Details
RT1-A3	haplotype	N/A	microsatellite markers, polymerase chain reaction	EAE	Disease risk	Approximately 45% of the LEW. NR2 and LEWR1 displayed this relapsing–remitting pattern. Relapses were evident to a lower degree in LEW.NR3 and the parental LEW.N strain.Lymph node cells from rMOG(a.a.1-125)/IFA-immunized LEW.N, LEW.LR1, LEW.NR2 and LEW.NR3 rats responded to rMOG(a.a.1-125) stimulation in vitro with a relatively high number of IFN-g secreting cells. In contrast, there was no detectable T cell response in cultures derived from LEW and LEW. NR1 rats .In rats induced with the MBPGP63-88 peptide/CFA only LEW and LEW.NR1 rats, but not LEW.N, LEW.LR1, LEW. NR2 and LEW.NR3 rats, had detectable IFN-g responses upon restimulation with the immunizing peptide.We measured titers of antigen-specific antibodies in sera 12 days p.i.Susceptible strains raised significantly higher antibody titers than the resistant strains .Th1 (IgG2b) and Th2 (IgG1)-associated immunoglobulin isotypes were similarly affected in resistant and susceptible strains, demonstrating that there is no bias towards a Th2-like antibody response in the resistant strains.Immunization with recombinant myelin oligodendrocyte glycoprotein (a.a.1-125; MOG)/IFA induced EAE in strains expressing the MHC class II allele RT1.Bn , whereas strains expressing the RT1.Bl were resistant. In myelin basic protein peptide (MBPGP63-88)/CFA-induced EAE, RT1.Bl expressing strains were susceptible whereas strains expressing the RT1.Bn were resistant. High levels of antigen-specific IFN-g secreting lymphoid cells and antigen-specific serum IgG antibodies were only recorded in rats with an MHC class II allele that permitted MOG- or MBP-EAE, respectively.	N/A	15748954	Details
TNF	promoter polymorphism	TNF-376A	microsatellite study	MS	Disease risk	This study was designed as a reappraisal of the association between the TNF-376A promoter polymorphism and susceptibility to multiple sclerosis found in the Spanish population but not in other populations	because of the higher frequency of an extended, conserved haplotype carrying the TNF-376A allele.	15007139	Details
NRG1	SNP	rs7014762	mismatch PCR-RFLP	MS	Disease risk	No significant difference in the allelic and genotype frequencies of the NRG1 polymorphism between MS patients and control group in Iranian population.	Neuregulin 1 (NRG1) is a signaling protein that mediates cell–cell interactions and plays critical roles in the growth of the nervous system. This gene has isoforms which are generated through alternative splicing and different promoter usage.	25802071	Details
NRG1	SNP	rs7014762	mismatch PCR-RFLP	MS	Phenotypic risk	Considering rs7014762 polymorphism frequencies, significant difference was observed between primary progressive MS group in comparison to the control group.	Neuregulin 1 (NRG1) is a signaling protein that mediates cell–cell interactions and plays critical roles in the growth of the nervous system. This gene has isoforms which are generated through alternative splicing and different promoter usage.	25802071	Details
CCR5	allele	CCR5 Delta32	modified multiplex PCR	MS	Disease risk	There was no significant difference in the prevalence of CCR5 D32 in patients and controls.	Multiple sclerosis (MS) is characterized by T cell and monocyte infiltration in the central nervous system.The CC chemokine receptor CCR5 has been implicated in the pathogenesis of MS as mononuclear cells.	17511851	Details
CCR5	polymorphism	promoter -2459	modified multiplex PCR	MS	Disease risk	There was no significant difference in the prevalence of the CCR5 promoter -2459 genotypes in patients and controls.	Multiple sclerosis (MS) is characterized by T cell and monocyte infiltration in the central nervous system.The CC chemokine receptor CCR5 has been implicated in the pathogenesis of MS as mononuclear cells.	17511851	Details
CCR5	allele	CCR5 Delta32	modified multiplex PCR	MS	Treatment risk	The CCR5 D32 allele was not associated with attack risk in patients with MS treated with IFN-b.	Multiple sclerosis (MS) is characterized by T cell and monocyte infiltration in the central nervous system.The CC chemokine receptor CCR5 has been implicated in the pathogenesis of MS as mononuclear cells.	17511851	Details
CCR5	polymorphism	promoter -2459	modified multiplex PCR	MS	Treatment risk	The attack risk was not associated with the CCR5 promoter genotype in this sample of IFN-b-treated MS patients.	Multiple sclerosis (MS) is characterized by T cell and monocyte infiltration in the central nervous system.The CC chemokine receptor CCR5 has been implicated in the pathogenesis of MS as mononuclear cells.	17511851	Details
HLA-DRB1	methylation-mediated SNP	rs9267649	MSRE-qPCR	MS	Disease risk	rs9267649 displayed a genome-wide significant association with MS with a similar protective effect in all cohorts .	Genetic variants in the loci encoding epigenetic machinery genes have been associated with MS suggesting a role for epigenetic mechanisms in disease pathology.	29921915	Details
BDNF	SNP	rs6265	MX4000 (Stratagene) real-time thermal cycler	MS	Disease risk	Based on the overlapping regions from the VBM and TFCE method, we surmise that regions in the cingulate have higher GM volumes in MS patients with the Met66 allele of BDNF.	N/A	20478698	Details
HLA-DQB1	polymorphisms	*0601	N/A	MS	Disease risk	DQB Gene Frequency Analysis of 116 Unrelated Patients With Multiple Sclerosis (MSU)* and 32 Related Patients With Multiple Sclerosis(MSR), 23 Parents (Pa) and 27 Siblings (Si) of Patients With MSR, and 86 Healthy Controls (C)	N/A	8442703	Details
HLA-DRB1	polymorphisms	DRw8	N/A	MS	Disease risk	These differences were not significant when corrected for the number of antigens tested.	N/A	3492235	Details
HLA-DRB1	polymorphisms	DRB1*1201	N/A	MS	Disease risk	Carriage frequencies of HLA-DRB1 alleles in MS vs controls by 2-digit and 4-digit HLA genotyping	N/A	20207784	Details
HLA-DQB1	polymorphisms	*0201	N/A	MS	Disease risk	Among the DQB genes, the DQB1 *0502 allele was diminished in patients with MSr vs controls (Pc=.04),while the sum of DQB1*0201 and *0302 alleles was significantly in reased in patients with MSR vs controls (Pc=.003).	N/A	8442703	Details
HLA-DRB1	polymorphisms	DRw9	N/A	MS	Disease risk	These differences were not significant when corrected for the number of antigens tested.	N/A	3492235	Details
HLA-DRB1	polymorphisms	DRB1*1301	N/A	MS	Disease risk	In addition to the known risk allele HLA-DRB1*1501, evidence of increased susceptibility to MS was found for three additional alleles, DRB1*0405, DRB1*1104 and DRB1*1303, though the power was insufficient to sustain significance for these when crudely Bonferroni corrected over all alleles considered.	N/A	20207784	Details
IL6	allele	A1,A2,A3,A4,A5,A6,A7,A8d,A9	N/A	MS	Disease risk	None of these were associated with in globo susceptibility to MS.	N/A	11196678	Details
HLA-DQB1	polymorphisms	*0301	N/A	MS	Disease risk	DQB Gene Frequency Analysis of 116 Unrelated Patients With Multiple Sclerosis (MSU)* and 32 Related Patients With Multiple Sclerosis(MSR), 23 Parents (Pa) and 27 Siblings (Si) of Patients With MSR, and 86 Healthy Controls (C)	N/A	8442703	Details
HLA-DRB1	polymorphisms	DRw10	N/A	MS	Disease risk	These differences were not significant when corrected for the number of antigens tested.	N/A	3492235	Details
HLA-DRB1	polymorphisms	DRB1*1302	N/A	MS	Disease risk	Carriage frequencies of HLA-DRB1 alleles in MS vs controls by 2-digit and 4-digit HLA genotyping	N/A	20207784	Details
IL6	allele	A1,A2,A3,A4,A5,A6,A7,A8d,A9	N/A	MS	Phenotypic risk	Analysis of clinically different groups showed that the A5 allele was associated with a benign but not with a malignant course of disease.In particular, the frequency of the A5/A5 genotype was significantly higher in patients with benign MS.In addition, carriage of any of the larger alleles (A6->A9) was associated with accelerated onset of disease.	Part of this beneficial effect has been attributed to the ability of this cytokine to induce protease inhibitors.	11196678	Details
HLA-DQB1	polymorphisms	*0302	N/A	MS	Disease risk	Among the DQB genes, the DQB1 *0502 allele was diminished in patients with MSr vs controls (Pc=.04),while the sum of DQB1*0201 and *0302 alleles was significantly in reased in patients with MSR vs controls (Pc=.003).	N/A	8442703	Details
HLA-DRB1	polymorphisms	DRw1	N/A	MS	Disease risk	This raises the possibility of a significant association between HLA-DQwl and MS.	N/A	3492235	Details
HLA-DRB1	polymorphisms	DRB1*1303	N/A	MS	Disease risk	Carriage frequencies of HLA-DRB1 alleles in MS vs controls by 2-digit and 4-digit HLA genotyping	N/A	20207784	Details
HLA-DQB1	polymorphisms	*0402	N/A	MS	Disease risk	DQB Gene Frequency Analysis of 116 Unrelated Patients With Multiple Sclerosis (MSU)* and 32 Related Patients With Multiple Sclerosis(MSR), 23 Parents (Pa) and 27 Siblings (Si) of Patients With MSR, and 86 Healthy Controls (C)	N/A	8442703	Details
HLA-DRB1	polymorphisms	DR1	N/A	MS	Phenotype risk	no significant HLA associations were found with age of onset of disease or initial symptoms.	N/A	3492235	Details
HLA-DRB1	polymorphisms	DRB1*1401	N/A	MS	Disease risk	Carriage frequencies of HLA-DRB1 alleles in MS vs controls by 2-digit and 4-digit HLA genotyping	N/A	20207784	Details
HLA-DQB1	polymorphisms	*0501	N/A	MS	Disease risk	DQB Gene Frequency Analysis of 116 Unrelated Patients With Multiple Sclerosis (MSU)* and 32 Related Patients With Multiple Sclerosis(MSR), 23 Parents (Pa) and 27 Siblings (Si) of Patients With MSR, and 86 Healthy Controls (C)	N/A	8442703	Details
HLA-DRB1	polymorphisms	DR2	N/A	MS	Phenotype risk	no significant HLA associations were found with age of onset of disease or initial symptoms.	N/A	3492235	Details
HLA-DRB1	polymorphisms	DRB1*1501	N/A	MS	Disease risk	In addition to the known risk allele HLA-DRB1*1501, evidence of increased susceptibility to MS was found for three additional alleles, DRB1*0405, DRB1*1104 and DRB1*1303, though the power was insufficient to sustain significance for these when crudely Bonferroni corrected over all alleles considered.	N/A	20207784	Details
HLA-DQB1	polymorphisms	*0502	N/A	MS	Disease risk	Among the DQB genes, the DQB1 *0502 allele was diminished in patients with MSr vs controls (Pc=.04),while the sum of DQB1*0201 and *0302 alleles was significantly in reased in patients with MSR vs controls (Pc=.003).	N/A	8442703	Details
HLA-DRB1	polymorphisms	DR3	N/A	MS	Phenotype risk	no significant HLA associations were found with age of onset of disease or initial symptoms.	N/A	3492235	Details
HLA-DRB1	polymorphisms	DRB1*1502	N/A	MS	Disease risk	Carriage frequencies of HLA-DRB1 alleles in MS vs controls by 2-digit and 4-digit HLA genotyping	N/A	20207784	Details
IL18	SNP	rs187238	N/A	MS	Disease risk	Genotype C/C polymorphism rs187238 locus IL-18 gene associated with frequent exacerbations of relapsing-remitting multiple sclerosis, high speed of progression of the disease and is characterized by marked changes in latency of peak V ABR and VEP P100.	N/A	24300807	Details
HLA-DQB1	polymorphisms	*0503	N/A	MS	Disease risk	DQB Gene Frequency Analysis of 116 Unrelated Patients With Multiple Sclerosis (MSU)* and 32 Related Patients With Multiple Sclerosis(MSR), 23 Parents (Pa) and 27 Siblings (Si) of Patients With MSR, and 86 Healthy Controls (C)	N/A	8442703	Details
HLA-DRB1	polymorphisms	DR4	N/A	MS	Phenotype risk	no significant HLA associations were found with age of onset of disease or initial symptoms.	N/A	3492235	Details
HLA-DRB1	polymorphisms	DRB1*1601	N/A	MS	Disease risk	Carriage frequencies of HLA-DRB1 alleles in MS vs controls by 2-digit and 4-digit HLA genotyping	N/A	20207784	Details
KIR2DL1	N/A	N/A	N/A	MS	Disease risk	Significantly higher frequencies were found for KIR2DL5 and KIR3DS1 genes in MS patients and the carriage of the KIR2DL1 gene was associated with a higher progression index.	N/A	21665278	Details
HLA-DQB1	polymorphisms	*0601	N/A	MS	Disease risk	DQB Gene Frequency Analysis of 116 Unrelated Patients With Multiple Sclerosis (MSU)* and 32 Related Patients With Multiple Sclerosis(MSR), 23 Parents (Pa) and 27 Siblings (Si) of Patients With MSR, and 86 Healthy Controls (C)	N/A	8442703	Details
HLA-DRB1	polymorphisms	DR5	N/A	MS	Phenotype risk	no significant HLA associations were found with age of onset of disease or initial symptoms.	N/A	3492235	Details
HLA-B	HLA-Bw4	N/A	N/A	MS	Disease risk	Significantly higher frequencies were found for KIR2DL5 and KIR3DS1 genes in MS patients and the carriage of the KIR2DL1 gene was associated with a higher progression index.	N/A	21665278	Details
HLA-DQB1	polymorphisms	*0602	N/A	MS	Disease risk	DQB Gene Frequency Analysis of 116 Unrelated Patients With Multiple Sclerosis (MSU)* and 32 Related Patients With Multiple Sclerosis(MSR), 23 Parents (Pa) and 27 Siblings (Si) of Patients With MSR, and 86 Healthy Controls (C)	N/A	8442703	Details
HLA-DRB1	polymorphisms	DRw6	N/A	MS	Phenotype risk	no significant HLA associations were found with age of onset of disease or initial symptoms.	N/A	3492235	Details
HLA-DQB1	polymorphisms	*0603	N/A	MS	Disease risk	DQB Gene Frequency Analysis of 116 Unrelated Patients With Multiple Sclerosis (MSU)* and 32 Related Patients With Multiple Sclerosis(MSR), 23 Parents (Pa) and 27 Siblings (Si) of Patients With MSR, and 86 Healthy Controls (C)	N/A	8442703	Details
HLA-DRB1	polymorphisms	DR7	N/A	MS	Phenotype risk	no significant HLA associations were found with age of onset of disease or initial symptoms.	N/A	3492235	Details
HLA-DRB1	polymorphisms	DRB1*01	N/A	MS	Disease risk	P-values from PDT analyses of DRB1 in MS families	N/A	16905561	Details
APOE	genotype	E o4	N/A	MS	Disease risk	APOE o4 polymorphism is not associated with a more severe clinical course and does not appear to influence recovery of exacerbations.	APOE is a glycoprotein involved in lipid transport and cholesterol homeostasis; moreover, it is the major lipid carrier in the brain.	16459715	Details
HLA-DRB1	polymorphisms	DRw8	N/A	MS	Phenotype risk	no significant HLA associations were found with age of onset of disease or initial symptoms.	N/A	3492235	Details
HLA-DRB1	polymorphisms	DRB1*03	N/A	MS	Disease risk	P-values from PDT analyses of DRB1 in MS families	N/A	16905561	Details
CD6	SNP	rs3019561	N/A	MS	Disease risk	We identified association of haplotypes composed of two non synonymous SNPs [rs11230563 (R225W) and rs2074225(A257V)] in the 2nd SRCR domain with susceptibility to MS.	CD6 is a cell surface scavenger receptor involved in T-cell activation and proliferation, as well as in thymocyte differentiation.	23638056	Details
HLA-DRB1	polymorphisms	DRw9	N/A	MS	Phenotype risk	no significant HLA associations were found with age of onset of disease or initial symptoms.	N/A	3492235	Details
HLA-DRB1	polymorphisms	DRB1*04	N/A	MS	Disease risk	P-values from PDT analyses of DRB1 in MS families	N/A	16905561	Details
CD6	SNP	rs3019562	N/A	MS	Disease risk	We identified association of haplotypes composed of two non synonymous SNPs [rs11230563 (R225W) and rs2074225(A257V)] in the 2nd SRCR domain with susceptibility to MS.	CD6 is a cell surface scavenger receptor involved in T-cell activation and proliferation, as well as in thymocyte differentiation.	23638056	Details
HLA-DRB1	polymorphisms	DRw10	N/A	MS	Phenotype risk	no significant HLA associations were found with age of onset of disease or initial symptoms.	N/A	3492235	Details
HLA-DRB1	polymorphisms	DRB1*07	N/A	MS	Disease risk	P-values from PDT analyses of DRB1 in MS families	N/A	16905561	Details
IL2RA	SNP	rs2104286	N/A	MS	Disease risk	One association between the rs2104286 (A vs G contrast) polymorphism of the interleukin 2RA (IL2RA) gene and increased MS susceptibility was initially supported by highly suggestive evidence	N/A	35526474	Details
CD6	SNP	rs3019548	N/A	MS	Disease risk	We identified association of haplotypes composed of two non synonymous SNPs [rs11230563 (R225W) and rs2074225(A257V)] in the 2nd SRCR domain with susceptibility to MS.	CD6 is a cell surface scavenger receptor involved in T-cell activation and proliferation, as well as in thymocyte differentiation.	23638056	Details
HLA-DRB1	polymorphisms	DRw1	N/A	MS	Phenotype risk	no significant HLA associations were found with age of onset of disease or initial symptoms.	N/A	3492235	Details
HLA-DRB1	polymorphisms	DRB1*08	N/A	MS	Disease risk	P-values from PDT analyses of DRB1 in MS families	N/A	16905561	Details
SPP1	SNP	rs1126616	N/A	MS	Disease risk	When global and one-by-one comparisons between both groups were made, no significant differences were observed.No differences were apparent when allelic or phenotypic (carrier) frequencies were compared instead.	Osteopontin (OPN) is a Th1 cytokine with multiple functions in inflammation and immunity, and in bone metabolism.	17439891	Details
IL2RA	SNP	rs12722489	N/A	MS	Disease risk	We also identified that two associations of IL2RA gene (rs2104286 poly颅 morphism [AA vs AG + GG contrast] and rs12722489 polymorphism [C vs T contrast] with MS risk was also graded as suggestive in the main analysis.	the rs12722489 polymorphism in the IL2RA gene is associated with an increased risk of disease,	35526474	Details
GRIN1	clone	anti-LGI1	N/A	MS	Disease risk	The Most Common Clone of Anti-NMDAR Encephalitis Was Not Found in Healthy People Nor Patients With Anti-LGI1 Encephalitis, MS, or NMOSD	N/A	32849520	Details
CD6	SNP	rs2905506	N/A	MS	Disease risk	We identified association of haplotypes composed of two non synonymous SNPs [rs11230563 (R225W) and rs2074225(A257V)] in the 2nd SRCR domain with susceptibility to MS.	CD6 is a cell surface scavenger receptor involved in T-cell activation and proliferation, as well as in thymocyte differentiation.	23638056	Details
IL1RN	polymorphisms	VNTR	N/A	MS	Disease risk	Our results showed no significant differences in the distribution of these polymorphisms between MS patients and controls.	N/A	19876593	Details
HLA-DRB1	polymorphisms	DRB1*09	N/A	MS	Disease risk	P-values from PDT analyses of DRB1 in MS families	N/A	16905561	Details
IL7R	SNP	rs987107	N/A	MS	Disease risk	The remaining four associations with suggestive evidence were associated with rs987107 and T244 polymorphisms of the IL7R gene.	N/A	35526474	Details
GRIN1	clone	NMOSD	N/A	MS	Disease risk	The Most Common Clone of Anti-NMDAR Encephalitis Was Not Found in Healthy People Nor Patients With Anti-LGI1 Encephalitis, MS, or NMOSD	N/A	32849520	Details
CD6	SNP	rs11230548	N/A	MS	Disease risk	We identified association of haplotypes composed of two non synonymous SNPs [rs11230563 (R225W) and rs2074225(A257V)] in the 2nd SRCR domain with susceptibility to MS.	CD6 is a cell surface scavenger receptor involved in T-cell activation and proliferation, as well as in thymocyte differentiation.	23638056	Details
IL1B	polymorphisms	-511	N/A	MS	Disease risk	Our results showed no significant differences in the distribution of these polymorphisms between MS patients and controls.	N/A	19876593	Details
HLA-DRB1	polymorphisms	DRB1*010	N/A	MS	Disease risk	P-values from PDT analyses of DRB1 in MS families	N/A	16905561	Details
IL7R	SNP	T244	N/A	MS	Disease risk	The remaining four associations with suggestive evidence were associated with rs987107 and T244 polymorphisms of the IL7R gene.	N/A	35526474	Details
CD6	SNP	rs17824933	N/A	MS	Disease risk	We identified association of haplotypes composed of two non synonymous SNPs [rs11230563 (R225W) and rs2074225(A257V)] in the 2nd SRCR domain with susceptibility to MS.	CD6 is a cell surface scavenger receptor involved in T-cell activation and proliferation, as well as in thymocyte differentiation.	23638056	Details
IL1B	polymorphisms	+3,953	N/A	MS	Disease risk	Our results showed no significant differences in the distribution of these polymorphisms between MS patients and controls.	N/A	19876593	Details
HLA-DRB1	polymorphisms	DRB1*11	N/A	MS	Disease risk	P-values from PDT analyses of DRB1 in MS families	N/A	16905561	Details
CD6	SNP	rs11230555	N/A	MS	Disease risk	We identified association of haplotypes composed of two non synonymous SNPs [rs11230563 (R225W) and rs2074225(A257V)] in the 2nd SRCR domain with susceptibility to MS.	CD6 is a cell surface scavenger receptor involved in T-cell activation and proliferation, as well as in thymocyte differentiation.	23638056	Details
IL1RN	polymorphisms	VNTR	N/A	MS	Phenotype risk	Furthermore, stratification for clinical characteristics, such as age at disease onset, clinical course, sex, and severity did not provide significant differences between patients and controls.	N/A	19876593	Details
HLA-DRB1	polymorphisms	DRB1*12	N/A	MS	Disease risk	P-values from PDT analyses of DRB1 in MS families	N/A	16905561	Details
CD6	SNP	rs916811	N/A	MS	Disease risk	We identified association of haplotypes composed of two non synonymous SNPs [rs11230563 (R225W) and rs2074225(A257V)] in the 2nd SRCR domain with susceptibility to MS.	CD6 is a cell surface scavenger receptor involved in T-cell activation and proliferation, as well as in thymocyte differentiation.	23638056	Details
IL1B	polymorphisms	-511	N/A	MS	Phenotype risk	Furthermore, stratification for clinical characteristics, such as age at disease onset, clinical course, sex, and severity did not provide significant differences between patients and controls.	N/A	19876593	Details
HLA-DRB1	polymorphisms	DRB1*13	N/A	MS	Disease risk	P-values from PDT analyses of DRB1 in MS families	N/A	16905561	Details
CD6	SNP	rs11230559	N/A	MS	Disease risk	We identified association of haplotypes composed of two non synonymous SNPs [rs11230563 (R225W) and rs2074225(A257V)] in the 2nd SRCR domain with susceptibility to MS.	CD6 is a cell surface scavenger receptor involved in T-cell activation and proliferation, as well as in thymocyte differentiation.	23638056	Details
IL1B	polymorphisms	+3,953	N/A	MS	Phenotype risk	Furthermore, stratification for clinical characteristics, such as age at disease onset, clinical course, sex, and severity did not provide significant differences between patients and controls.	N/A	19876593	Details
HLA-DRB1	polymorphisms	DRB1*14	N/A	MS	Disease risk	P-values from PDT analyses of DRB1 in MS families	N/A	16905561	Details
CD6	SNP	rs2237997	N/A	MS	Disease risk	We identified association of haplotypes composed of two non synonymous SNPs [rs11230563 (R225W) and rs2074225(A257V)] in the 2nd SRCR domain with susceptibility to MS.	CD6 is a cell surface scavenger receptor involved in T-cell activation and proliferation, as well as in thymocyte differentiation.	23638056	Details
HLA-DRB1	polymorphisms	DRB1*15	N/A	MS	Disease risk	Results derived from analyses of 1339 MS families indicate DRB1 variation influences MS susceptibility in a complex manner. DRB1*15 was strongly associated in families, and a dominant DRB1*15 dose effect was confirmed.	N/A	16905561	Details
VDR	SNP	N/A	N/A	MS	Disease risk	VDR genotypes were not associated with MS risk.	The metabolism of vitamin D is carried out through a series of hydroxylation reactions in the liver and kidneys catalyzed by members of the cytochrome p450 family. The primary bioactive metabolite 1,25(OH)2D exerts its effect through association with the vitamin D receptor (VDR), which is found on a variety of cell types, including cells in the immune system.It is plausible that genes that are involved in vitamin D metabolism, transport or activity may be related to risk of MS or modify the association between environmental or dietary exposure to MS.	20007432	Details
CD6	SNP	rs11230563	N/A	MS	Disease risk	We identified association of haplotypes composed of two non synonymous SNPs [rs11230563 (R225W) and rs2074225(A257V)] in the 2nd SRCR domain with susceptibility to MS.	CD6 is a cell surface scavenger receptor involved in T-cell activation and proliferation, as well as in thymocyte differentiation.	23638056	Details
HLA-DRB1	polymorphisms	DRB1*16	N/A	MS	Disease risk	P-values from PDT analyses of DRB1 in MS families	N/A	16905561	Details
CD6	SNP	rs2074225	N/A	MS	Disease risk	We identified association of haplotypes composed of two non synonymous SNPs [rs11230563 (R225W) and rs2074225(A257V)] in the 2nd SRCR domain with susceptibility to MS.	CD6 is a cell surface scavenger receptor involved in T-cell activation and proliferation, as well as in thymocyte differentiation.	23638056	Details
HLA-DRB1	polymorphisms	DRB1*15	N/A	MS	Phenotypic risk	In contrast, results obtained from 2201 MS cases argue convincingly that DRB1*15 genotypes do not modulate age of onset, or significantly influence disease severity measured using expanded disease disability score and disease duration.	N/A	16905561	Details
CD6	SNP	rs12360861	N/A	MS	Disease risk	We identified association of haplotypes composed of two non synonymous SNPs [rs11230563 (R225W) and rs2074225(A257V)] in the 2nd SRCR domain with susceptibility to MS.	CD6 is a cell surface scavenger receptor involved in T-cell activation and proliferation, as well as in thymocyte differentiation.	23638056	Details
ERVW-1	CNV	MSRV	N/A	MS	Phenotypic risk	MSRV increases its copy number in PBMC of MS patients and particularly in women with high clinical scores.	N/A	23308264	Details
CTLA4	SNP	rs221775A>G	N/A	MS	Disease risk	With current evidence, CTLA-4 gene rs221775A>G single nucleotide polymorphism had no association with the susceptibility of multiple sclerosis	N/A	28352806	Details
CD6	SNP	rs650258(5)	N/A	MS	Disease risk	We identified association of haplotypes composed of two non synonymous SNPs [rs11230563 (R225W) and rs2074225(A257V)] in the 2nd SRCR domain with susceptibility to MS.	CD6 is a cell surface scavenger receptor involved in T-cell activation and proliferation, as well as in thymocyte differentiation.	23638056	Details
ANKRD55	SNP	rs6859219	N/A	MS	Disease risk	Though the genetic association of DHCR7 with MS does not reach genome wide significance, ANKRD55 shows an unusually strong association with MS in this Spanish dataset.	N/A	22130326	Details
DHCR7	SNP	rs12785878	N/A	MS	Disease risk	The G allele of rs12785878, which is associated with lower levels of 25(OH)D and risk for T1D, enhances susceptibility to MS.	N/A	22130326	Details
AFF3	SNP	rs11676922	N/A	MS	Disease risk	Summary of association results in the joint Spanish multiple sclerosis dataset	N/A	22130326	Details
CCR6	SNP	rs6859219	N/A	MS	Disease risk	Summary of association results in the joint Spanish multiple sclerosis dataset	N/A	22130326	Details
CYP2R1	SNP	rs10741657	N/A	MS	Disease risk	Summary of association results in the joint Spanish multiple sclerosis dataset	N/A	22130326	Details
IL2RA	SNP	rs706778	N/A	MS	Disease risk	Summary of association results in the joint Spanish multiple sclerosis dataset	N/A	22130326	Details
B2m	Deletion	class I-deficient (β2m/)	N/A	persistent demyelination	Disease risk	There was extensive demyelination in the spinal cords of chronically infected class I-deficient and class II-deficient mice of the identical resistant H–2b genotype.	Alterations in the cytokines secreted and the distributions of T cells present in the lesions of class I-deficient mice may contribute to the absence of neurologic deficit following demyelination.	9461192	Details
IL10	SNP	rs3024505	N/A	MS	Disease risk	Summary of association results in the joint Spanish multiple sclerosis dataset	N/A	22130326	Details
PRDM1	SNP	rs548234	N/A	MS	Disease risk	Summary of association results in the joint Spanish multiple sclerosis dataset	N/A	22130326	Details
TNFRSF6B	SNP	rs4809330(*)A	N/A	MS	Disease risk	Polymorphisms related with TNFRSF6B, were associated with MS risk.	T-cell receptor engagement without costimulation leads to suboptimal T-cell activation and T-cell anergy.Two main superfamilies of co-signalling molecules based on their structure modulate the T-cell response: the immunoglobulin superfamily and the tumour necrosis factor receptor superfamily (TNFRSF).One of these TNFRSF members is HVEM (herpes virus entry mediator or TNFRSF14), a molecular switch that regulates the host immune response depending on which ligand it binds.	20962851	Details
PRDM1	SNP	rs7746082	N/A	MS	Disease risk	Summary of association results in the joint Spanish multiple sclerosis dataset	N/A	22130326	Details
TNFRSF14	SNP	rs6684865(*)A	N/A	MS	Disease risk	The frequencies of the common allele and common genotype of rs6684865 were significantly higher in MS patients than in healthy controls.	T-cell receptor engagement without costimulation leads to suboptimal T-cell activation and T-cell anergy.Two main superfamilies of co-signalling molecules based on their structure modulate the T-cell response: the immunoglobulin superfamily and the tumour necrosis factor receptor superfamily (TNFRSF).One of these TNFRSF members is HVEM (herpes virus entry mediator or TNFRSF14), a molecular switch that regulates the host immune response depending on which ligand it binds.	20962851	Details
PXK	SNP	rs13315591	N/A	MS	Disease risk	Summary of association results in the joint Spanish multiple sclerosis dataset	N/A	22130326	Details
HLA-DRB1	polymorphisms	DRB1*1501	N/A	MS	Disease risk	Conversion to MS was positively associated with the DRB1*1501.DQA1*0102.DQBl*0602 haplotype, but the influence of HLA was only significant in patients with disseminated brain lesions at presentation (MRI positive); MS developed in 86% of MRI-positive, DRBl*1501-positive patients compared with 55% of MRI -positive, DRB 1 * 1501-negative patients.	N/A	8244781	Details
IL6	SNP	rs2069852	N/A	N/A	Disease risk	No interactions were found with IL-6 and BCL-2 SNP GG genotypes.	N/A	36725329	Details
HLA-DQA1	polymorphisms	DQA1*0102	N/A	MS	Disease risk	Conversion to MS was positively associated with the DRB1*1501.DQA1*0102.DQBl*0602 haplotype, but the influence of HLA was only significant in patients with disseminated brain lesions at presentation (MRI positive); MS developed in 86% of MRI-positive, DRBl*1501-positive patients compared with 55% of MRI -positive, DRB 1 * 1501-negative patients.	N/A	8244781	Details
BCL2	SNP	rs2187163	N/A	N/A	Disease risk	No interactions were found with IL-6 and BCL-2 SNP GG genotypes.	N/A	36725329	Details
HLA-DQB1	polymorphisms	DQB1*0602	N/A	MS	Disease risk	Conversion to MS was positively associated with the DRB1*1501.DQA1*0102.DQBl*0602 haplotype, but the influence of HLA was only significant in patients with disseminated brain lesions at presentation (MRI positive); MS developed in 86% of MRI-positive, DRBl*1501-positive patients compared with 55% of MRI -positive, DRB 1 * 1501-negative patients.	N/A	8244781	Details
NFKB1	SNP	rs7665090	N/A	N/A	Disease risk	There was significant additive interaction between exposure to weed control products and NFKB1 SNP GG (attributable proportions (AP) 0.48, 95% CI 0.10 to 0.87), and exposure to plant or disease control products and absence of HLA-A*02 (AP 0.56; 95% CI 0.03 to 1.08).	N/A	36725329	Details
CBLB	SNP	rs9657904	N/A	MS	Disease risk	It was found that in this sample also, the common allele T of rs9657904 is significantly positively associated (one-tailed p7.35310-5) and with a comparable effect size with MS (OR1.31, 95% CI 1.14 to 1.52).	N/A	21037273	Details
IGH	SNP	rs11621145	N/A	MS	Disease risk	We found that rs11621145 showed statistically significant evidence for association with susceptibility to MS.	N/A	25392328	Details
MC1R	the red hair color (RHC) variant	Arg151Cys, Arg160Trp, Asp294His	N/A	MS	Disease risk	Individually, only the Arg160Trp variant was associated with increased MS risk.The association between RHC variant genotype and MS was more evident for women than for men.	N/A	18711112	Details
SPON1	SNP	rs7104613T	N/A	MS	Phenotypic risk	Specifically, in PMS we found evidence of association for the rs7104613 T in gene SPON1, which was associated with a reduction of DeepGMV and was the only marker withstanding multiple testing correction according to our estimated number of effective tests.	N/A	33864731	Details
HLA-DRA	polymorphism	HLA-DR15	N/A	MS	Phenotypic risk	In addition, there was a suggestion that the association with HLA-DR15 was greater in patients with both pars planitis and multiple sclerosis.	N/A	10080220	Details
SEMA3A	SNP	rs740948A	N/A	MS	Phenotypic risk	For RRMS, clustering of phenotypes revealed hierarchically grouped associations for the GM volumetric measures driven by variants in SEMA3A and GRIN2B loci, with evidence of association between rs740948A in SEMA3A and higher WMV, whereas the variant rs7970177T in GRIN2B is associated with decreased volume of deep GM.	N/A	33864731	Details
HLA-DRA	polymorphism	HLA-DR16	N/A	MS	Phenotypic risk	In addition, there was a suggestion that the association with HLA-DR15 was greater in patients with both pars planitis and multiple sclerosis.	N/A	10080220	Details
IGHG1	polymorphism	IgG CG1	N/A	MS	Disease risk	We report here the results of restriction fragment length polymorphisms (RFLP) analysis of the constant gene regions of immunoglobulin gamma (IgG C) 1, 2 and 3 in MS patients and controls, using the restriction enzymes TaqI, PvulI and BstEII. No significant differences were observed, regardless of subgrouping of patients according to clinical disease type or HLA class II phenotype.	N/A	8096224	Details
IGHG1	polymorphism	IgG CG2	N/A	MS	Disease risk	We report here the results of restriction fragment length polymorphisms (RFLP) analysis of the constant gene regions of immunoglobulin gamma (IgG C) 1, 2 and 3 in MS patients and controls, using the restriction enzymes TaqI, PvulI and BstEII. No significant differences were observed, regardless of subgrouping of patients according to clinical disease type or HLA class II phenotype.	N/A	8096224	Details
CD40	SNP	rs6074022	N/A	MS	Disease risk	The "case-control" research in Russian Altai territory population has proved that DR15 and DR3 as well as the combination of female sex and alleles A of TNFα of rs1800629 locus are associated with high risk of multiple sclerosis. The relationship between disease and CD40 polymorphism (rs6074022) was not found.	N/A	21666592	Details
IGHG1	polymorphism	IgG CG3	N/A	MS	Disease risk	We report here the results of restriction fragment length polymorphisms (RFLP) analysis of the constant gene regions of immunoglobulin gamma (IgG C) 1, 2 and 3 in MS patients and controls, using the restriction enzymes TaqI, PvulI and BstEII. No significant differences were observed, regardless of subgrouping of patients according to clinical disease type or HLA class II phenotype.	N/A	8096224	Details
TNF	allel	A	N/A	MS	Disease risk	The "case-control" research in Russian Altai territory population has proved that DR15 and DR3 as well as the combination of female sex and alleles A of TNFα of rs1800629 locus are associated with high risk of multiple sclerosis. The relationship between disease and CD40 polymorphism (rs6074022) was not found.	N/A	21666592	Details
VDR	polymorphisms	C_3290614_10(A/T)	N/A	MS	Disease risk	None of the individual SNP’s assays showed evidence for association with susceptibility to multiple sclerosis. Analysis of the four marker haplotypes was equally disappointing.	N/A	15311355	Details
SELP	SNP	rs6133	N/A	MS	Disease risk	No significant differences in either allelic or genotypic frequency in all the SNPs tested were found in the Italian population. A tendency to an increased frequency of the rs6133 T allele was observed in the American population, but applying the Bonferroni correction the significance threshold was not reached.	the selectin gene cluster studied likely does not influence the susceptibility to MS in Caucasians.	19240957	Details
VDR	polymorphisms	C_8716062_10(C/T)	N/A	MS	Disease risk	None of the individual SNP’s assays showed evidence for association with susceptibility to multiple sclerosis. Analysis of the four marker haplotypes was equally disappointing.	N/A	15311355	Details
SELL	SNP	rs4987310	N/A	MS	Disease risk	Combining the two SNPs, we found no difference in haplotype distribution in patients compared with controls, either in Italian or in American population.	the selectin gene cluster studied likely does not influence the susceptibility to MS in Caucasians.	19240957	Details
VDR	polymorphisms	C_12060044_1_(A/G)	N/A	MS	Disease risk	None of the individual SNP’s assays showed evidence for association with susceptibility to multiple sclerosis. Analysis of the four marker haplotypes was equally disappointing.	N/A	15311355	Details
SELE	SNP	rs5368	N/A	MS	Disease risk	Combining the two SNPs, we found no difference in haplotype distribution in patients compared with controls, either in Italian or in American population.	the selectin gene cluster studied likely does not influence the susceptibility to MS in Caucasians.	19240957	Details
VDR	polymorphisms	C_2880811_10(C/T)	N/A	MS	Disease risk	None of the individual SNP’s assays showed evidence for association with susceptibility to multiple sclerosis. Analysis of the four marker haplotypes was equally disappointing.	N/A	15311355	Details
MCAT	allele	K*	N/A	MS	Disease risk	The K haplotype shows association with MS after correction for multiple testing.	Among variants defining the K haplotype, the A→G transition at nt9055 changes alanine to threonine in the ATP6 subunit of complex V or F0F1-ATPase, while the A→G transition at nt10,398 changes threonine to alanine in the ND3 subunit of Complex I.	18708297	Details
MCAT	allele	J*	N/A	MS	Disease risk	The K haplotype shows association with MS after correction for multiple testing.	N/A	18708297	Details
Abl2	SNP	rs30466582	N/A	EAE	Disease risk	The Non-synonymous SNP rs30466582 Does Not Influence Arg Actin Binding Affinity	N/A	29550852	Details
HLA-DRB1	polymorphisms	DRB1*1501	N/A	MS	Disease risk	These results have implications for the role of hMBP as relevant autoantigen, and of DRB1*1501 as susceptibility allele in MS.	N/A	7679413	Details
HLA-DRB1	polymorphisms	DRB1*1501	N/A	MS	Disease risk	The present study shows that, in Scandinavians, MS is associated with DRB1*1501, DQAI*0201, and DQBl*0602.	N/A	1349586	Details
HLA-DQA1	polymorphisms	DQA1*0201	N/A	MS	Disease risk	The present study shows that, in Scandinavians, MS is associated with DRB1*1501, DQAI*0201, and DQBl*0602.	N/A	1349586	Details
HLA-DQB1	polymorphisms	DQB1*0602	N/A	MS	Disease risk	The present study shows that, in Scandinavians, MS is associated with DRB1*1501, DQAI*0201, and DQBl*0602.	N/A	1349586	Details
HLA-DPA1	polymorphisms	DPA1*0103	N/A	MS	Disease risk	The frequencies in MS of DPw4- associated DNA fragments were not significantly increased although the RR of DPAI*0103 was 2.9 (not significant) and DPB1*04 was 2.5 (not significant).	N/A	1349586	Details
HLA-DPB1	polymorphisms	DPB1*04	N/A	MS	Disease risk	The frequencies in MS of DPw4- associated DNA fragments were not significantly increased although the RR of DPAI*0103 was 2.9 (not significant) and DPB1*04 was 2.5 (not significant).	N/A	1349586	Details
HLA-DRB1	allele	HLA-DRB1*15:01	N/A	MS	Disease risk	Evidence for interaction between pregnancy exposure and established genetic risk variants, including the strongly associated HLA-DRB1*15:01 allele and a weighted genetic risk score, was not observed. Results from sensitivity analyses were consistent with observed results.	N/A	33037103	Details
HLA-DQB1	polymorphism	DQB1*0302	N/A	EAE	Phenotypic risk	This would suggest that the presence of more than one susceptible allele, namely HLA DRB1*1502 and DQB1*0302 resulted in enhanced severity of disease in the DRB1*1502/DQB1*0302 mice, possibly due to the additional selection and expansion of potential autoreactive T cells.	The other possible mechanism for the enhanced severity of disease in HLA DRB1*1502/DQB1*0302 mice may involve antigen presentation by specific HLA molecules as well as TCR repertoire selection.	16194572	Details
TNFSF14	genotype	rs1077667AA	N/A	MS	Disease risk	Carriers of the GG genotype had the lowest serum levels of LIGHT (p=0.02).	N/A	23037546	Details
HLA-DRB1	polymorphism	DRB1*1502	N/A	EAE	Phenotypic risk	This would suggest that the presence of more than one susceptible allele, namely HLA DRB1*1502 and DQB1*0302 resulted in enhanced severity of disease in the DRB1*1502/DQB1*0302 mice, possibly due to the additional selection and expansion of potential autoreactive T cells.	The other possible mechanism for the enhanced severity of disease in HLA DRB1*1502/DQB1*0302 mice may involve antigen presentation by specific HLA molecules as well as TCR repertoire selection.	16194572	Details
TNFSF14	genotype	rs1077667AG	N/A	MS	Disease risk	Carriers of the GG genotype had the lowest serum levels of LIGHT (p=0.02).	N/A	23037546	Details
HLA-C	polymorphisms	Cw1	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
TNFSF14	genotype	rs1077667GG	N/A	MS	Disease risk	Carriers of the GG genotype had the lowest serum levels of LIGHT (p=0.02).	N/A	23037546	Details
HLA-DRB1	polymorphisms	DR2	N/A	MS	Disease risk	An association of DR2 specificity of the DRBI gene with MS was found in the combined group of Kazakhs, Russians, and offsprings from mixed marriages.	N/A	21866867	Details
HLA-C	polymorphisms	Cw2	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
IL1B	polymorphisms	(-511 C/T)	N/A	MS	Disease risk	No significant differences were revealed in the distribution of the genotypes and in the frequencies of alleles at the polymorphic sites of the genes IL-1beta (-511 C/T), IL-2 (-475 A/T and -631 G/A), PON1 (M55L), and UCP2 (-866 G/A).	N/A	21866867	Details
HLA-C	polymorphisms	Cw3	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
HLA-DRB1	polymorphism	HLA-DRB1*15	N/A	MS	Disease risk	Month of birth, HLA-DRB1 genotype, and risk of multiple sclerosis are associated.	N/A	20018638	Details
IL2	polymorphisms	(-475 A/T)	N/A	MS	Disease risk	No significant differences were revealed in the distribution of the genotypes and in the frequencies of alleles at the polymorphic sites of the genes IL-1beta (-511 C/T), IL-2 (-475 A/T and -631 G/A), PON1 (M55L), and UCP2 (-866 G/A).	N/A	21866867	Details
HLA-C	polymorphisms	Cw4	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
IL2	polymorphisms	(-631 G/A)	N/A	MS	Disease risk	No significant differences were revealed in the distribution of the genotypes and in the frequencies of alleles at the polymorphic sites of the genes IL-1beta (-511 C/T), IL-2 (-475 A/T and -631 G/A), PON1 (M55L), and UCP2 (-866 G/A).	N/A	21866867	Details
HLA-C	polymorphisms	Cw5	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
IL6	polymorphisms	(-634 C/G)	N/A	MS	Disease risk	Statistically significant (p < 0.05) differences between the MS patients and healthy individuals were observed in the distribution of the genotypes at site -634 G/C of the IL-6 gene in the Kazakh group, in the allelic frequencies at site -308 A/G in the promoter region of the TNFalpha gene in the Russian group, and in the frequencies of alleles at the polymorphic Q 192R locus of the PON1 gene in the Kazakh group.	N/A	21866867	Details
HLA-C	polymorphisms	Cw6	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
PON1	polymorphisms	(M55L)	N/A	MS	Disease risk	No significant differences were revealed in the distribution of the genotypes and in the frequencies of alleles at the polymorphic sites of the genes IL-1beta (-511 C/T), IL-2 (-475 A/T and -631 G/A), PON1 (M55L), and UCP2 (-866 G/A).	N/A	21866867	Details
HLA-C	polymorphisms	Cw7	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
PON1	polymorphisms	(Q192R)	N/A	MS	Disease risk	Statistically significant (p < 0.05) differences between the MS patients and healthy individuals were observed in the distribution of the genotypes at site -634 G/C of the IL-6 gene in the Kazakh group, in the allelic frequencies at site -308 A/G in the promoter region of the TNFalpha gene in the Russian group, and in the frequencies of alleles at the polymorphic Q 192R locus of the PON1 gene in the Kazakh group.	N/A	21866867	Details
HLA-C	polymorphisms	Cw8	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
IL23R	SNP	rs10127763 rs6656929 rs10489630 rs1004819 rs790633 rs7517847 rs10489629 rs7528924 rs12070470 rs12030948 rs11465804 rs4655530 rs10789229 rs11209026 rs1343151 rs6693831 rs10889677 rs2863209 rs11209030 rs11209032 rs6660226 rs1495965 rs7539817 rs10889680 rs12	N/A	MS	Disease risk	We conclude that it is unlikely that the IL23R gene confers any significant risk for MS.	N/A	18164077	Details
UCP2	polymorphisms	(-866 G/A)	N/A	MS	Disease risk	No significant differences were revealed in the distribution of the genotypes and in the frequencies of alleles at the polymorphic sites of the genes IL-1beta (-511 C/T), IL-2 (-475 A/T and -631 G/A), PON1 (M55L), and UCP2 (-866 G/A).	N/A	21866867	Details
HLA-DRB1	polymorphisms	DR1	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
HLA-DRB1	polymorphisms	DR2	N/A	MS	Disease risk	No correlation between DR2 specificity and MS was found in the separately examined groups of Kazakhs and Russians.	N/A	21866867	Details
HLA-DRB1	polymorphisms	DR2	N/A	MS	Disease risk	Significant differences are found only for A3 and DR2, the latter showing a highly significant difference between controls and the phenotyped MS group.	N/A	3874450	Details
IL1B	polymorphisms	(-511 C/T)	N/A	MS	Disease risk	No significant differences were revealed in the distribution of the genotypes and in the frequencies of alleles at the polymorphic sites of the genes IL-1beta (-511 C/T), IL-2 (-475 A/T and -631 G/A), PON1 (M55L), and UCP2 (-866 G/A).	N/A	21866867	Details
HLA-DRB1	polymorphisms	DR3	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
TNF	polymorphisms	(-308 A/G)	N/A	MS	Disease risk	Statistically significant (p < 0.05) differences between the MS patients and healthy individuals were observed in the distribution of the genotypes at site -634 G/C of the IL-6 gene in the Kazakh group, in the allelic frequencies at site -308 A/G in the promoter region of the TNFalpha gene in the Russian group, and in the frequencies of alleles at the polymorphic Q 192R locus of the PON1 gene in the Kazakh group.	N/A	21866867	Details
HLA-DRB1	polymorphisms	DR4	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
HLA-DRB1	polymorphisms	DR5	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
HLA-DRB1	polymorphisms	DR6	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
HLA-DRB1	polymorphism	HLA-DRB1*04:05	N/A	MS	Disease risk	ICLs were negatively associated with the presence of the HLA-DRB1*04:05 allele.	N/A	28474969	Details
LRP2	allel	rs12988804*T	N/A	MS	Phenotypic risk	The rs12988804*T allele is associated with a 1.16-fold increased hazard rate for a relapse occurring (P = 0.0078) and a higher baseline relapse rate prior to immunomodulatory treatment (P = 0.044).	N/A	29303040	Details
HLA-DRB1	polymorphisms	DR7	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
HLA-DRB1	polymorphism	HLA-DRB1*15:01	N/A	MS	Disease risk	ICLs are associated with greater disease severity in Japanese MS patients and are partly suppressed by the HLA-DRB1*04:05 allele.	N/A	28474969	Details
HLA-A	polymorphisms	A1	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
HLA-A	polymorphisms	A2	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
HLA-A	polymorphisms	A3	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
CNR1	SNP	RS1049353(GG/GA/AA)	N/A	MS	Disease risk	No associations were identified between these CNR1 variants and cognitive impairment in MS.	N/A	17942526	Details
HLA-A	polymorphisms	A11	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
CNR1	SNP	RS806377(GG/GA/AA)	N/A	MS	Disease risk	No associations were identified between these CNR1 variants and cognitive impairment in MS.	N/A	17942526	Details
HLA-A	polymorphisms	A23	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
CNR1	SNP	RS806380(TT/TC/CC)	N/A	MS	Disease risk	No associations were identified between these CNR1 variants and cognitive impairment in MS.	N/A	17942526	Details
HLA-A	polymorphisms	A24	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
CYP24A1	genotype	rs2248359 GG	N/A	MS	Disease risk	In patients with MS and in the control, the GA genotype CYP24A1 (rs2248359) was associated with a 25(OH)D level of less than 30 ng/ml.	N/A	32844632	Details
HLA-A	polymorphisms	A25	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
CYP24A1	genotype	rs2248359 GA	N/A	MS	Disease risk	In patients with MS and in the control, the GA genotype CYP24A1 (rs2248359) was associated with a 25(OH)D level of less than 30 ng/ml.	N/A	32844632	Details
HLA-A	polymorphisms	A26	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
CYP24A1	genotype	rs2248359 AA	N/A	MS	Disease risk	In patients with MS and in the control, the GA genotype CYP24A1 (rs2248359) was associated with a 25(OH)D level of less than 30 ng/ml.	N/A	32844632	Details
HLA-A	polymorphisms	A28	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
CYP24A1	allel	rs2248359 G	N/A	MS	Disease risk	In patients with MS and in the control, the GA genotype CYP24A1 (rs2248359) was associated with a 25(OH)D level of less than 30 ng/ml.	N/A	32844632	Details
HLA-A	polymorphisms	A29	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
SLC9A9	SNP	rs2801	N/A	MS	Disease risk	We discovered differential SLC9A9 expression in different brain regions and identified 15 rs9828519-tagged SNPs that significantly regulated SLC9A9 expression only in occipital cortex, intralobular white matter, and substantia nigra.	SLC9A9 encodes a sodium/proton exchanger that is a member of the solute carrier 9 protein families.	27766536	Details
CYP24A1	allel	rs2248359 A	N/A	MS	Disease risk	In patients with MS and in the control, the GA genotype CYP24A1 (rs2248359) was associated with a 25(OH)D level of less than 30 ng/ml.	N/A	32844632	Details
HLA-A	polymorphisms	A30+31	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
SLC9A9	SNP	rs2800	N/A	MS	Disease risk	We discovered differential SLC9A9 expression in different brain regions and identified 15 rs9828519-tagged SNPs that significantly regulated SLC9A9 expression only in occipital cortex, intralobular white matter, and substantia nigra.	SLC9A9 encodes a sodium/proton exchanger that is a member of the solute carrier 9 protein families.	27766536	Details
CYP27B1	genotype	rs703842 TT	N/A	MS	Disease risk	A relationship between the MS risk and the TC genotype CYP27B1 (rs703842) was identified.	N/A	32844632	Details
HLA-A	polymorphisms	A32	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
SLC9A9	SNP	rs4240552	N/A	MS	Disease risk	We discovered differential SLC9A9 expression in different brain regions and identified 15 rs9828519-tagged SNPs that significantly regulated SLC9A9 expression only in occipital cortex, intralobular white matter, and substantia nigra.	SLC9A9 encodes a sodium/proton exchanger that is a member of the solute carrier 9 protein families.	27766536	Details
CYP27B1	genotype	rs703842 TC	N/A	MS	Disease risk	A relationship between the MS risk and the TC genotype CYP27B1 (rs703842) was identified.	N/A	32844632	Details
HLA-A	polymorphisms	Aw33	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
SLC9A9	SNP	rs6440183	N/A	MS	Disease risk	We discovered differential SLC9A9 expression in different brain regions and identified 15 rs9828519-tagged SNPs that significantly regulated SLC9A9 expression only in occipital cortex, intralobular white matter, and substantia nigra.	SLC9A9 encodes a sodium/proton exchanger that is a member of the solute carrier 9 protein families.	27766536	Details
CYP27B1	genotype	rs703842 CC	N/A	MS	Disease risk	A relationship between the MS risk and the TC genotype CYP27B1 (rs703842) was identified.	N/A	32844632	Details
HLA-B	polymorphisms	B5	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
EVI5	SNP	rs79667032	N/A	MS	disease risk	We identified nine best non-MHC independent SNPs (r2<0.70 within a windows size of 100Kb), which were not previously identified by IMSGC and hence represent novel suggestive MS variants.	N/A	28933650	Details
SLC9A9	SNP	rs6440184	N/A	MS	Disease risk	We discovered differential SLC9A9 expression in different brain regions and identified 15 rs9828519-tagged SNPs that significantly regulated SLC9A9 expression only in occipital cortex, intralobular white matter, and substantia nigra.	SLC9A9 encodes a sodium/proton exchanger that is a member of the solute carrier 9 protein families.	27766536	Details
CYP27B1	allel	rs703842 T	N/A	MS	Disease risk	A relationship between the MS risk and the TC genotype CYP27B1 (rs703842) was identified.	N/A	32844632	Details
HLA-B	polymorphisms	B7	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
IGSF3	SNP	rs517857	N/A	MS	disease risk	We identified nine best non-MHC independent SNPs (r2<0.70 within a windows size of 100Kb), which were not previously identified by IMSGC and hence represent novel suggestive MS variants.	N/A	28933650	Details
SLC9A9	SNP	rs10709029	N/A	MS	Disease risk	We discovered differential SLC9A9 expression in different brain regions and identified 15 rs9828519-tagged SNPs that significantly regulated SLC9A9 expression only in occipital cortex, intralobular white matter, and substantia nigra.	SLC9A9 encodes a sodium/proton exchanger that is a member of the solute carrier 9 protein families.	27766536	Details
CYP27B1	allel	rs703842 C	N/A	MS	Disease risk	A relationship between the MS risk and the TC genotype CYP27B1 (rs703842) was identified.	N/A	32844632	Details
HLA-B	polymorphisms	B8	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
LINC02868	SNP	rs11583823	N/A	MS	disease risk	We identified nine best non-MHC independent SNPs (r2<0.70 within a windows size of 100Kb), which were not previously identified by IMSGC and hence represent novel suggestive MS variants.	N/A	28933650	Details
SLC9A9	SNP	rs7625330	N/A	MS	Disease risk	We discovered differential SLC9A9 expression in different brain regions and identified 15 rs9828519-tagged SNPs that significantly regulated SLC9A9 expression only in occipital cortex, intralobular white matter, and substantia nigra.	SLC9A9 encodes a sodium/proton exchanger that is a member of the solute carrier 9 protein families.	27766536	Details
HLA-B	polymorphisms	B12	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
RUNX3	SNP	rs335555	N/A	MS	disease risk	We identified nine best non-MHC independent SNPs (r2<0.70 within a windows size of 100Kb), which were not previously identified by IMSGC and hence represent novel suggestive MS variants.	N/A	28933650	Details
SLC9A9	SNP	rs9828519	N/A	MS	Disease risk	We discovered differential SLC9A9 expression in different brain regions and identified 15 rs9828519-tagged SNPs that significantly regulated SLC9A9 expression only in occipital cortex, intralobular white matter, and substantia nigra.	SLC9A9 encodes a sodium/proton exchanger that is a member of the solute carrier 9 protein families.	27766536	Details
HLA-B	polymorphisms	B13	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
KIF5A	SNP	rs1678542	N/A	MS	Disease risk	Our results, in addition to validating some of these loci as risk factors for MS, are consistent with shared genetic mechanisms underlying different immune-mediated diseases.	the common and specific associated genes in the different immune-mediated diseases will be crucial in future attempts at shaping the contribution of each pathway to the different disorders and the identification of novel therapies	20508602	Details
TRPC3	SNP	rs55756717	N/A	MS	disease risk	We identified nine best non-MHC independent SNPs (r2<0.70 within a windows size of 100Kb), which were not previously identified by IMSGC and hence represent novel suggestive MS variants.	N/A	28933650	Details
SLC9A9	SNP	rs1900647	N/A	MS	Disease risk	We discovered differential SLC9A9 expression in different brain regions and identified 15 rs9828519-tagged SNPs that significantly regulated SLC9A9 expression only in occipital cortex, intralobular white matter, and substantia nigra.	SLC9A9 encodes a sodium/proton exchanger that is a member of the solute carrier 9 protein families.	27766536	Details
HLA-B	polymorphisms	B14	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
SH2B3	SNP	rs3184504	N/A	MS	Disease risk	Our results, in addition to validating some of these loci as risk factors for MS, are consistent with shared genetic mechanisms underlying different immune-mediated diseases.	the common and specific associated genes in the different immune-mediated diseases will be crucial in future attempts at shaping the contribution of each pathway to the different disorders and the identification of novel therapies	20508602	Details
SIM1	SNP	rs924974	N/A	MS	disease risk	We identified nine best non-MHC independent SNPs (r2<0.70 within a windows size of 100Kb), which were not previously identified by IMSGC and hence represent novel suggestive MS variants.	N/A	28933650	Details
SLC9A9	SNP	rs1900648	N/A	MS	Disease risk	We discovered differential SLC9A9 expression in different brain regions and identified 15 rs9828519-tagged SNPs that significantly regulated SLC9A9 expression only in occipital cortex, intralobular white matter, and substantia nigra.	SLC9A9 encodes a sodium/proton exchanger that is a member of the solute carrier 9 protein families.	27766536	Details
HLA-B	polymorphisms	B15	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
CD226	SNP	rs763361	N/A	MS	Disease risk	Our results, in addition to validating some of these loci as risk factors for MS, are consistent with shared genetic mechanisms underlying different immune-mediated diseases.	the common and specific associated genes in the different immune-mediated diseases will be crucial in future attempts at shaping the contribution of each pathway to the different disorders and the identification of novel therapies	20508602	Details
OPCML	SNP	rs2659624	N/A	MS	disease risk	We identified nine best non-MHC independent SNPs (r2<0.70 within a windows size of 100Kb), which were not previously identified by IMSGC and hence represent novel suggestive MS variants.	N/A	28933650	Details
SLC9A9	SNP	rs11919382	N/A	MS	Disease risk	We discovered differential SLC9A9 expression in different brain regions and identified 15 rs9828519-tagged SNPs that significantly regulated SLC9A9 expression only in occipital cortex, intralobular white matter, and substantia nigra.	SLC9A9 encodes a sodium/proton exchanger that is a member of the solute carrier 9 protein families.	27766536	Details
PTPN22	polymorphisms	620W	N/A	MS	Phenotypic risk	these analyses do not exclude a role for the PTPN22 allele in susceptibility to CD or MS.	N/A	16391555	Details
HLA-B	polymorphisms	B17	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
LAIR2	SNP	rs2161471	N/A	MS	disease risk	We identified nine best non-MHC independent SNPs (r2<0.70 within a windows size of 100Kb), which were not previously identified by IMSGC and hence represent novel suggestive MS variants.	N/A	28933650	Details
SLC9A9	SNP	rs1122452	N/A	MS	Disease risk	We discovered differential SLC9A9 expression in different brain regions and identified 15 rs9828519-tagged SNPs that significantly regulated SLC9A9 expression only in occipital cortex, intralobular white matter, and substantia nigra.	SLC9A9 encodes a sodium/proton exchanger that is a member of the solute carrier 9 protein families.	27766536	Details
HLA-B	polymorphisms	B18	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
SLC9A9	SNP	rs1562495	N/A	MS	Disease risk	We discovered differential SLC9A9 expression in different brain regions and identified 15 rs9828519-tagged SNPs that significantly regulated SLC9A9 expression only in occipital cortex, intralobular white matter, and substantia nigra.	SLC9A9 encodes a sodium/proton exchanger that is a member of the solute carrier 9 protein families.	27766536	Details
HLA-B	polymorphisms	B21	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
HLA-DRB1	SNP	HLA-DRB1*15:01(+)*04:05()	N/A	MS	disease risk	Our study suggests that distinct HLA-DRB1 alleles could differentially influence brain and lesion volumes over the disease course of MS.	HLA-DRB1*15 augments the extent of inflammation in cortical lesions.	32247967	Details
SLC9A9	SNP	rs6440185	N/A	MS	Disease risk	We discovered differential SLC9A9 expression in different brain regions and identified 15 rs9828519-tagged SNPs that significantly regulated SLC9A9 expression only in occipital cortex, intralobular white matter, and substantia nigra.	SLC9A9 encodes a sodium/proton exchanger that is a member of the solute carrier 9 protein families.	27766536	Details
HLA-B	polymorphisms	Bw22	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
HLA-DRB1	SNP	HLA-DRB1*15:01()*04:05(+)	N/A	MS	disease risk	Our study suggests that distinct HLA-DRB1 alleles could differentially influence brain and lesion volumes over the disease course of MS.	HLA-DRB1*15 augments the extent of inflammation in cortical lesions.	32247967	Details
SLC9A9	SNP	rs4839655	N/A	MS	Disease risk	We discovered differential SLC9A9 expression in different brain regions and identified 15 rs9828519-tagged SNPs that significantly regulated SLC9A9 expression only in occipital cortex, intralobular white matter, and substantia nigra.	SLC9A9 encodes a sodium/proton exchanger that is a member of the solute carrier 9 protein families.	27766536	Details
HLA-B	polymorphisms	B27	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
HLA-A	polymorphisms	A1	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
HLA-B	polymorphisms	B35	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
HLA-A	polymorphisms	A2	N/A	MS	Disease risk	A2 and B12 significantly decreased.	N/A	6978384	Details
HLA-B	polymorphisms	B37	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
HLA-A	polymorphisms	A3	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
HLA-B	polymorphisms	B38	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
HLA-A	polymorphisms	A9	N/A	MS	Disease risk	A9 and B7 were found significantly increased in the MS group as a whole.	N/A	6978384	Details
HLA-B	polymorphisms	B39	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
HLA-A	polymorphisms	A10	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
HLA-B	polymorphisms	B40	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
HLA-A	polymorphisms	A11	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
HLA-B	polymorphisms	B41	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
HLA-A	polymorphisms	AW19	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
HLA-B	polymorphisms	B47	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
HLA-A	polymorphisms	AW24	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
HLA-B	polymorphisms	Bw53	N/A	MS	Disease risk	Differences observed are not significant.	N/A	3874450	Details
HLA-A	polymorphisms	A25	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
HLA-A	polymorphisms	A26	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
HLA-A	polymorphisms	A28	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
HLA-A	polymorphisms	A29	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
HLA-A	polymorphisms	AW30	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
APOE	polymorphism	E2	N/A	MS	Disease risk	There were no differences in apoE allele frequencies in MS or herpes zoster patients compared to the allele frequencies of controls.	N/A	10949525	Details
HLA-A	polymorphisms	AW31	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
APOE	polymorphism	E3	N/A	MS	Disease risk	There were no differences in apoE allele frequencies in MS or herpes zoster patients compared to the allele frequencies of controls.	N/A	10949525	Details
HLA-A	polymorphisms	AW32	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
APOE	polymorphism	E4	N/A	MS	Disease risk	There were no differences in apoE allele frequencies in MS or herpes zoster patients compared to the allele frequencies of controls.	N/A	10949525	Details
HLA-A	polymorphisms	AW33	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
HLA-DQB1	polymorphism	DQBl*0201	N/A	MS	Disease risk	we conclude that Caucasian and Sardinian populations share HLA-DQB1 'k0201 and 'k0302 alleles in genetic susceptibility to MS.	N/A	1565247	Details
DDT	SNP	rs755622	N/A	MS	Disease risk	Te results show that the minor allele frequency of rs755622 and expression of DDT are signifcantly increased in males for MS subjects and this minor allele variant can signifcantly upregulate DDT expression for males but not females, which suggests that the regulation of DDT expression level by rs755622 can afect MS progression in males.	N/A	30140701	Details
HLA-B	polymorphisms	B5	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
HLA-DQB1	polymorphism	DQBl*0301	N/A	MS	Disease risk	we conclude that Caucasian and Sardinian populations share HLA-DQB1 'k0201 and 'k0302 alleles in genetic susceptibility to MS.	N/A	1565247	Details
CBLB	SNP	rs9657904	N/A	MS	Disease risk	A genome-wide association scan of ~6.6 million genotyped or imputed variants in 882 Sardinian individuals with multiple sclerosis (cases) and 872 controls suggested association of CBLB gene variants with disease, which was confirmed in 1,775 cases and 2,005 controls (rs9657904, overall P = 1.60 × 1010,OR = 1.40).	rs9657904 might affect CBLB splicing and/or transcription reguation and could provide mechanistic clues for the observed disease association.	20453840	Details
TRB	Haplotype assignments	N/A	N/A	MS	disease risk	The reported MS association with the TCR-β gene complex therefore does not appear to be due to genes within the diversity, joining, or constant region but more likely involves a specific gene(s) within the variable region.	N/A	1674514	Details
HLA-B	polymorphisms	B7	N/A	MS	Disease risk	A9 and B7 were found significantly increased in the MS group as a whole.	N/A	6978384	Details
HLA-DQB1	polymorphism	DQBl*0302	N/A	MS	Disease risk	we conclude that Caucasian and Sardinian populations share HLA-DQB1 'k0201 and 'k0302 alleles in genetic susceptibility to MS.	N/A	1565247	Details
3p14–13	N/A	N/A	N/A	MS	Phenotypic risk	We conclude that support was obtained for the location of a gene or genes with importance for MS susceptibility in 3p14–13 region.	N/A	11781712	Details
BTN1A1	alloantigens	BT 101	N/A	MS	disease risk	1 of the B-cell antigens, BT 101, was found in 49 out of 59 patients (83%), compared with 10 out of 30 normal individuals (33%), giving a relative risk of 9·8 times to the association.	N/A	63743	Details
HLA-B	polymorphisms	B8	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
HLA-DQB1	polymorphism	DQBl*0501	N/A	MS	Disease risk	we conclude that Caucasian and Sardinian populations share HLA-DQB1 'k0201 and 'k0302 alleles in genetic susceptibility to MS.	N/A	1565247	Details
HLA-B	alloantigens	HLA-B7	N/A	MS	disease risk	2 other B-cell alloantigens and HLA-B7 showed lesser but significant positive associations with M.S.	N/A	63743	Details
HLA-B	polymorphisms	B12	N/A	MS	Disease risk	A2 and B12 significantly decreased.	N/A	6978384	Details
HLA-DQB1	polymorphism	DQBl*0502	N/A	MS	Disease risk	we conclude that Caucasian and Sardinian populations share HLA-DQB1 'k0201 and 'k0302 alleles in genetic susceptibility to MS.	N/A	1565247	Details
IGH	polymorphism	IghC	N/A	MS	N/A	The H24 probe, containing the S region for the heavy chain M, exhibits close linkage with Gm markers for G1 and G3, presumably because regions homolo- gous to the S region of M are closely associated with most lghC genes.	N/A	8423203	Details
HLA-B	polymorphisms	B13	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
HLA-DQB1	polymorphism	DQBl*0601	N/A	MS	Disease risk	we conclude that Caucasian and Sardinian populations share HLA-DQB1 'k0201 and 'k0302 alleles in genetic susceptibility to MS.	N/A	1565247	Details
HLA-B	polymorphisms	B14	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
HLA-DQB1	polymorphism	DQBl*0602	N/A	MS	Disease risk	we conclude that Caucasian and Sardinian populations share HLA-DQB1 'k0201 and 'k0302 alleles in genetic susceptibility to MS.	N/A	1565247	Details
TRB	allele	Vβ1I（25kb）	N/A	MS	Disease risk	However one Vβl I , 25 kb allele and a haplotype defined by Vβl I and Cβ alleles showed a correlation with MS susceptibility of borderline significance.	N/A	8105988	Details
HLA-B	polymorphisms	B15	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
P2RX7	SNP	rs17525809	N/A	MS	Disease risk	The case-control analysis with 734 MS samples and 588 controls showed an association between the T allele of rs17525809 and the disease which remained significant after correction for multiple testing by 10,000 permutations.	N/A	21906809	Details
TRB	allele	Cβ	N/A	MS	Disease risk	However one Vβl I , 25 kb allele and a haplotype defined by Vβl I and Cβ alleles showed a correlation with MS susceptibility of borderline significance.	N/A	8105988	Details
HLA-B	polymorphisms	BW16	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
P2RX7	SNP	rs208294	N/A	MS	Disease risk	Case-control analysis of selected SNPs of the P2X7 receptor gene in the whole cohort.	N/A	21906809	Details
TRB	allele	Vβ1I	N/A	MS	Disease risk	However one Vβl I , 25 kb allele and a haplotype defined by Vβl I and Cβ alleles showed a correlation with MS susceptibility of borderline significance.	N/A	8105988	Details
HLA-B	polymorphisms	B17	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
P2RX7	SNP	rs1718119	N/A	MS	Disease risk	Case-control analysis of selected SNPs of the P2X7 receptor gene in the whole cohort.	N/A	21906809	Details
HLA-A	allele	HLA-A3	N/A	MS	Disease risk	Therefore, the HLA-D locus is probably closely related to the locus that deter- mines the group 4 antigen. In contrast,HLA-B7 is almost completely included in the group 4 antigen among MS patients, but not among the normal population.	The antiserums defining the five other B lymphocyte specificities reacted at a lower frequency to B cells from multiple sclerosis patients, showing that increased reactivity to group 4 antiserums was specific.	1085490	Details
HLA-A	polymorphisms	HLA-A*31:01	N/A	MS	Disease risk	Further investigations of this peptide revealed that the binding of C-terminal residue of this peptide has a more significant effect on binding to this allele than the N-terminal part of the peptide.	N/A	32242486	Details
HLA-B	polymorphisms	B18	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
P2RX7	polymorphism	TA	N/A	MS	Disease risk	In turn, we observed that rs17525809 is in LD with rs208294 and that the CG haplotype they form is less frequentinMS than in controls.	N/A	21906809	Details
HLA-B	allele	HLA-B7	N/A	MS	Disease risk	Therefore, the HLA-D locus is probably closely related to the locus that deter- mines the group 4 antigen. In contrast,HLA-B7 is almost completely included in the group 4 antigen among MS patients, but not among the normal population.	The antiserums defining the five other B lymphocyte specificities reacted at a lower frequency to B cells from multiple sclerosis patients, showing that increased reactivity to group 4 antiserums was specific.	1085490	Details
HLA-B	polymorphisms	BW21	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
P2RX7	polymorphism	TG	N/A	MS	Disease risk	In turn, we observed that rs17525809 is in LD with rs208294 and that the CG haplotype they form is less frequentinMS than in controls.	N/A	21906809	Details
HLA-B	polymorphisms	BW35	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
P2RX7	polymorphism	CG	N/A	MS	Disease risk	In turn, we observed that rs17525809 is in LD with rs208294 and that the CG haplotype they form is less frequentinMS than in controls.	N/A	21906809	Details
HLA-B	polymorphisms	B27	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
P2RX7	polymorphism	AACCTG	N/A	MS	Disease risk	Case-control analysis of haplotypes formed by rs17525809 and rs208294 of P2X7 receptor gene in the whole cohort.	N/A	21906809	Details
HLA-B	polymorphisms	BW35	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
GRIK2	polymorphism	GCGc	N/A	MS	Disease risk	Case-control analysis of haplotypes formed by rs17525809 and rs208294 of P2X7 receptor gene in the whole cohort.	N/A	21906809	Details
FUT1	alleles	N/A	N/A	MS	Disease risk	with the O blood group. At least two genes, FUT1 and FUT2, encoding alpha (1,2) fucosyltransferases, control this complex epistatic effect.	encoding alpha fucosyltransferases	19204267	Details
HLA-B	polymorphisms	B37	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
GRIK2	polymorphism	CGGTGAT	N/A	MS	Disease risk	Case-control analysis of haplotypes formed by rs17525809 and rs208294 of P2X7 receptor gene in the whole cohort.	N/A	21906809	Details
FUT2	alleles	N/A	N/A	MS	Disease risk	with the O blood group. At least two genes, FUT1 and FUT2, encoding alpha (1,2) fucosyltransferases, control this complex epistatic effect.	encoding alpha fucosyltransferases	19204267	Details
HLA-B	polymorphisms	BW38	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
HLA-DRB1	polymorphism	HLA-DRB1*15	N/A	MS	Disease risk	In HLA-DRB1 analyses HLA-DRB1*15:01 was a stronger risk factor for OCB positive than OCB negative MS, whereas HLA-DRB1*04:04 was associated with increased risk of OCB negative MS and reduced risk of OCB positive MS.	N/A	23472185	Details
HLA-B	polymorphisms	BW39	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
HLA-DRB1	polymorphism	HLA-DRB1*04	N/A	MS	Disease risk	In HLA-DRB1 analyses HLA-DRB1*15:01 was a stronger risk factor for OCB positive than OCB negative MS, whereas HLA-DRB1*04:04 was associated with increased risk of OCB negative MS and reduced risk of OCB positive MS.	N/A	23472185	Details
HLA-B	polymorphisms	B40	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
MYO3B	SNP	N/A	N/A	MS	N/A	To ensure the power to detect variants with a modest effect size, we further analyzed 10 variants in 899 Finnish cases and 1325 controls, and in a total of 1521 cases and 1476 controls from Denmark, Norway and Sweden, but found no association. Our results thereby do not support a major function of the tested MYO9B variants in MS.	N/A	19142207	Details
HLA-DRB1	polymorphisms	DR1	N/A	MS	Disease risk	DR1, DRW6, and DR7 were decreased in MS and DR3 was increased.	N/A	6978384	Details
MYO3B	SNP	N/A	N/A	MS	N/A	To ensure the power to detect variants with a modest effect size, we further analyzed 10 variants in 899 Finnish cases and 1325 controls, and in a total of 1521 cases and 1476 controls from Denmark, Norway and Sweden, but found no association. Our results thereby do not support a major function of the tested MYO9B variants in MS.	N/A	19142207	Details
HLA-DRB1	polymorphisms	DR2	N/A	MS	Disease risk	a significant increase of DR2 in MS.	N/A	6978384	Details
HLA-DRB1	polymorphisms	DR3	N/A	MS	Disease risk	DR1, DRW6, and DR7 were decreased in MS and DR3 was increased.	N/A	6978384	Details
HLA-DRB1	polymorphisms	DR4	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
HLA-DRB1	polymorphisms	DR5	N/A	MS	Disease risk	HLA-A AND HLA-B TYPING OF THE TOTAL MS POPULATION	N/A	6978384	Details
HLA-DRB1	polymorphisms	DRW6	N/A	MS	Disease risk	DR1, DRW6, and DR7 were decreased in MS and DR3 was increased.	N/A	6978384	Details
HLA-DRB1	polymorphisms	DR7	N/A	MS	Disease risk	DR1, DRW6, and DR7 were decreased in MS and DR3 was increased.	N/A	6978384	Details
HLA-DRB1	polymorphisms	A3-B7	N/A	MS	Disease risk	DR1, DRW6, and DR7 were decreased in MS and DR3 was increased.	N/A	6978384	Details
HLA-DRB1	polymorphisms	A1-B8	N/A	MS	Disease risk	PHENOTYPIC ASSOCIATIONS	N/A	6978384	Details
HLA-DRB1	polymorphisms	A2-B12	N/A	MS	Disease risk	an increase of B8-DR3 and a decrease of B12DR7 as well as a decrease in B35-DR1.	N/A	6978384	Details
HLA-DRB1	polymorphisms	B7-B8	N/A	MS	Disease risk	PHENOTYPIC ASSOCIATIONS	N/A	6978384	Details
HLA-DRB1	allele	N/A	N/A	MS	Phenotypic risk	Female/male distribution varied between the DR3/DR3 and DR4/DRY and between the DR3/DRX and DR4/DRY groups.An excess of paternally transmitted DR3 in affected but not in healthy offspring was found. No evidence of a PO effect in transmission of DR4 in affected or healthy sibs was found.A PO effect on DR3 transmission from fathers was evident in women but not in men. Moreover, an effect of two copies of the maternal non-transmitted DR3 genotype was found in DR3 females but not in males.	N/A	15452304	Details
HLA-DRB1	polymorphisms	A3-B7	N/A	MS	Disease risk	PHENOTYPIC ASSOCIATIONS	N/A	6978384	Details
HLA-DQB1	allele	N/A	N/A	MS	Phenotypic risk	Female/male distribution varied between the DR3/DR3 and DR4/DRY and between the DR3/DRX and DR4/DRY groups.An excess of paternally transmitted DR3 in affected but not in healthy offspring was found. No evidence of a PO effect in transmission of DR4 in affected or healthy sibs was found.A PO effect on DR3 transmission from fathers was evident in women but not in men. Moreover, an effect of two copies of the maternal non-transmitted DR3 genotype was found in DR3 females but not in males.	N/A	15452304	Details
HLA-DRB1	polymorphisms	A1-B8	N/A	MS	Disease risk	PHENOTYPIC ASSOCIATIONS	N/A	6978384	Details
PTPN22	SNP	1858 SNP	N/A	MS	Disease risk	In conclusion, our data suggest that the PTPN22 1858 SNP has no, or only a negligible effect on MS susceptibility in the Spanish population. However, a minor effect of the PTPN22 SNP cannot be ruled out, and this may only be verifiable in an extremely large data set.	The lymphoid-specific phosphatase (LYP), encoded by the PTPN22 gene, is important in negative control of T-cell activation and in T-cell development.	15765267	Details
HLA-DRB1	polymorphisms	A2-B12	N/A	MS	Disease risk	PHENOTYPIC ASSOCIATIONS	N/A	6978384	Details
HLA-DRB1	polymorphisms	B7-DR2	N/A	MS	Disease risk	When the remitting MS group was compared to the control group, B7, DR2 and B7-DR2 were found to be increased	N/A	6978384	Details
HLA-DRB1	polymorphisms	B8-DR3	N/A	MS	Disease risk	an increase of B8-DR3 and a decrease of B12DR7 as well as a decrease in B35-DR1.	N/A	6978384	Details
NOTCH4	SNP	rs422951	N/A	MS	Disease risk	Using a logistic regression model, SNP rs422951 in the NOTCH4 gene was independently associated with MS susceptibility.	N/A	21654846	Details
HLA-DRB1	polymorphisms	B12-DR7	N/A	MS	Disease risk	an increase of B8-DR3 and a decrease of B12DR7 as well as a decrease in B35-DR1.	N/A	6978384	Details
HLA-DQA2	SNP	rs3997849	N/A	MS	Disease risk	Using a logistic regression model, MHC Class II SNP rs3997849, susceptible alleles A and G was independently associated with MS susceptibility.	N/A	21654846	Details
HLA-DRB1	polymorphisms	B35-DR 1	N/A	MS	Disease risk	an increase of B8-DR3 and a decrease of B12DR7 as well as a decrease in B35-DR1.	N/A	6978384	Details
CFB	allele	N/A	N/A	MS	Disease risk	We found a significantly lower frequency of the Bf F allele of the polymorphic factor B system in patients with definite multiple sclerosis (MS) but a normal frequency in patients with optic neuritis or suspected MS.	N/A	6120306	Details
HLA-DRB1	polymorphisms	A3-B7-DR2	N/A	MS	Disease risk	PHENOTYPIC ASSOCIATIONS	N/A	6978384	Details
HLA-DRB1	polymorphisms	A1-B8-DR3	N/A	MS	Disease risk	when patients with severe MS were compared to controls they showed an increased proportion of DR3, B8-DR3 and A1-B8-DR3.	N/A	6978384	Details
HLA-DRB1	polymorphisms	A2-B12-DR7	N/A	MS	Disease risk	PHENOTYPIC ASSOCIATIONS	N/A	6978384	Details
TNF	polymorphisms	TNFa9	N/A	MS	Disease risk	The previously described DRB1*15(2) allele, the TNFa9 allele and the biallelic combination (CCR5d32,DRB1*04) were reidentified as MS-associated in Russians.	N/A	19894308	Details
HLA-DRB1	polymorphisms	DR2-DR3	N/A	MS	Disease risk	PHENOTYPIC ASSOCIATIONS	N/A	6978384	Details
HLA-DRB1	polymorphisms	DRB1*15(2)	N/A	MS	Disease risk	The previously described DRB1*15(2) allele, the TNFa9 allele and the biallelic combination (CCR5d32,DRB1*04) were reidentified as MS-associated in Russians.	N/A	19894308	Details
TNFSF10	SNP	rs4894559	N/A	MS	Disease risk	three SNPs showing uncorrected p values,0.05 were successfully replicated: rs4894559 in TRAIL gene; rs4872077, in TRAILR-1 gene; and rs1001793 in TRAILR-2 gene.	The TNF-related apoptosis inducing ligand (TRAIL)/TRAIL receptor system participates in crucial steps in immune cell activation or differentiation.	21814551	Details
CCR5	genotype	(CCR5d32,DRB1*04)	N/A	MS	Disease risk	The previously described DRB1*15(2) allele, the TNFa9 allele and the biallelic combination (CCR5d32,DRB1*04) were reidentified as MS-associated in Russians.	N/A	19894308	Details
TNFRSF10A	SNP	rs4872077	N/A	MS	Disease risk	three SNPs showing uncorrected p values,0.05 were successfully replicated: rs4894559 in TRAIL gene; rs4872077, in TRAILR-1 gene; and rs1001793 in TRAILR-2 gene.	The TNF-related apoptosis inducing ligand (TRAIL)/TRAIL receptor system participates in crucial steps in immune cell activation or differentiation.	21814551	Details
HLA-DRB1	genotype	(CCR5d32,DRB1*04)	N/A	MS	Disease risk	The previously described DRB1*15(2) allele, the TNFa9 allele and the biallelic combination (CCR5d32,DRB1*04) were reidentified as MS-associated in Russians.	N/A	19894308	Details
TNFRSF10B	SNP	rs1001793	N/A	MS	Disease risk	three SNPs showing uncorrected p values,0.05 were successfully replicated: rs4894559 in TRAIL gene; rs4872077, in TRAILR-1 gene; and rs1001793 in TRAILR-2 gene.	The TNF-related apoptosis inducing ligand (TRAIL)/TRAIL receptor system participates in crucial steps in immune cell activation or differentiation.	21814551	Details
TGFB1	genotype	(-509 TGFb1*C, DRB1*18(3),CTLA4*G)	N/A	MS	Disease risk	We also identified previously unknown MS-associated tri-allelic combinations: (-509 TGFb1*C, DRB1*18(3),CTLA4*G) and (-238TNF*B1, -308TNF*A2,CTLA4*G).	N/A	19894308	Details
TNFRSF10B	SNP	rs11779484	N/A	MS	Disease risk	Genotype frequencies of the TRAIL and TRAILR significant polymorphisms.	The TNF-related apoptosis inducing ligand (TRAIL)/TRAIL receptor system participates in crucial steps in immune cell activation or differentiation.	21814551	Details
CTLA4	genotype	(-509 TGFb1*C, DRB1*18(3),CTLA4*G)	N/A	MS	Disease risk	We also identified previously unknown MS-associated tri-allelic combinations: (-509 TGFb1*C, DRB1*18(3),CTLA4*G) and (-238TNF*B1, -308TNF*A2,CTLA4*G).	N/A	19894308	Details
TNFRSF10B	SNP	rs4460370	N/A	MS	Disease risk	Genotype frequencies of the TRAIL and TRAILR significant polymorphisms.	The TNF-related apoptosis inducing ligand (TRAIL)/TRAIL receptor system participates in crucial steps in immune cell activation or differentiation.	21814551	Details
HLA-DRB1	genotype	(-509 TGFb1*C, DRB1*18(3),CTLA4*G)	N/A	MS	Disease risk	We also identified previously unknown MS-associated tri-allelic combinations: (-509 TGFb1*C, DRB1*18(3),CTLA4*G) and (-238TNF*B1, -308TNF*A2,CTLA4*G).	N/A	19894308	Details
SCN10A	SNP	rs6801957	N/A	MS	Phenotypic risk	Two SCN10A polymorphisms in high linkage disequilibrium showed significant association with MSFC performance in patients with MS.	N/A	26740675	Details
TNFRSF10B	SNP	rs9314261	N/A	MS	Disease risk	Genotype frequencies of the TRAIL and TRAILR significant polymorphisms.	The TNF-related apoptosis inducing ligand (TRAIL)/TRAIL receptor system participates in crucial steps in immune cell activation or differentiation.	21814551	Details
LTA	genotype	(-238TNF*B1, -308TNF*A2,CTLA4*G)	N/A	MS	Disease risk	We also identified previously unknown MS-associated tri-allelic combinations: (-509 TGFb1*C, DRB1*18(3),CTLA4*G) and (-238TNF*B1, -308TNF*A2,CTLA4*G).	N/A	19894308	Details
SCN10A	SNP	rs6795970	N/A	MS	Phenotypic risk	Two SCN10A polymorphisms in high linkage disequilibrium showed significant association with MSFC performance in patients with MS.	N/A	26740675	Details
TNFRSF10B	SNP	rs3924519	N/A	MS	Disease risk	Genotype frequencies of the TRAIL and TRAILR significant polymorphisms.	The TNF-related apoptosis inducing ligand (TRAIL)/TRAIL receptor system participates in crucial steps in immune cell activation or differentiation.	21814551	Details
TNF	genotype	(-238TNF*B1, -308TNF*A2,CTLA4*G)	N/A	MS	Disease risk	We also identified previously unknown MS-associated tri-allelic combinations: (-509 TGFb1*C, DRB1*18(3),CTLA4*G) and (-238TNF*B1, -308TNF*A2,CTLA4*G).	N/A	19894308	Details
CYBB	SNP	rs72619425	N/A	MS	Disease risk	We identified SNPs in the human NOX2 (CYBB) gene that associated with the severity of MS, and significantly increased CYBB expression was recorded in PBMCs from both MS patients and from MS severity risk allele rs72619425-A carrying individuals.	N/A	27479807	Details
IL7R	haplotypes	Hap1	N/A	MS	Disease risk	We demonstrate that IL-7Rα is up-regulated in response to IFN β in vitro for haplotypes 1 and 2, but not 4.	N/A	20187771	Details
CTLA4	genotype	(-238TNF*B1, -308TNF*A2,CTLA4*G)	N/A	MS	Disease risk	We also identified previously unknown MS-associated tri-allelic combinations: (-509 TGFb1*C, DRB1*18(3),CTLA4*G) and (-238TNF*B1, -308TNF*A2,CTLA4*G).	N/A	19894308	Details
IL7R	haplotypes	Hap2	N/A	MS	Disease risk	We demonstrate that IL-7Rα is up-regulated in response to IFN β in vitro for haplotypes 1 and 2, but not 4.	N/A	20187771	Details
TNF	allel	rs1799964/C	N/A	MS	Phenotypic risk	For lead, there were six statistically significant environmental interactions identified: rs1799964/C (TNF-α), rs769178/T (TNF-β), rs2189480/T (VDR), rs3782905/C (VDR), rs4890785/T (MBP), and rs7412/T (APOE).	N/A	25137520	Details
IL7R	haplotypes	Hap3	N/A	MS	Disease risk	We demonstrate that IL-7Rα is up-regulated in response to IFN β in vitro for haplotypes 1 and 2, but not 4.	N/A	20187771	Details
LTA	allel	rs769178/T	N/A	MS	Phenotypic risk	For lead, there were six statistically significant environmental interactions identified: rs1799964/C (TNF-α), rs769178/T (TNF-β), rs2189480/T (VDR), rs3782905/C (VDR), rs4890785/T (MBP), and rs7412/T (APOE).	N/A	25137520	Details
IL7R	haplotypes	Hap4	N/A	MS	Disease risk	We demonstrate that IL-7Rα is up-regulated in response to IFN β in vitro for haplotypes 1 and 2, but not 4.	N/A	20187771	Details
VDR	allel	rs2189480/T	N/A	MS	Phenotypic risk	For lead, there were six statistically significant environmental interactions identified: rs1799964/C (TNF-α), rs769178/T (TNF-β), rs2189480/T (VDR), rs3782905/C (VDR), rs4890785/T (MBP), and rs7412/T (APOE).	N/A	25137520	Details
VDR	allel	rs3782905/C	N/A	MS	Phenotypic risk	For lead, there were six statistically significant environmental interactions identified: rs1799964/C (TNF-α), rs769178/T (TNF-β), rs2189480/T (VDR), rs3782905/C (VDR), rs4890785/T (MBP), and rs7412/T (APOE).	N/A	25137520	Details
TPH2	SNP	rs4570625– rs10506645 GC	N/A	MS	Disease risk	The haplotype rs4570625-rs10506645TT of TPH2 gene was associated with the risk of severe disability in primary progressive MS(PPMS), while haplotype rs4570625-rs10506645TC appeared to be protective against disability in secondary progressive MS (SPMS).	in melatonin biosynthesis pathway	22698518	Details
MBP	allel	rs4890785/T	N/A	MS	Phenotypic risk	For lead, there were six statistically significant environmental interactions identified: rs1799964/C (TNF-α), rs769178/T (TNF-β), rs2189480/T (VDR), rs3782905/C (VDR), rs4890785/T (MBP), and rs7412/T (APOE).	N/A	25137520	Details
TPH2	SNP	rs4570625– rs10506645 TT	N/A	MS	Disease risk	The haplotype rs4570625-rs10506645TT of TPH2 gene was associated with the risk of severe disability in primary progressive MS(PPMS), while haplotype rs4570625-rs10506645TC appeared to be protective against disability in secondary progressive MS (SPMS).	in melatonin biosynthesis pathway	22698518	Details
APOE	allel	rs7412/T	N/A	MS	Phenotypic risk	For lead, there were six statistically significant environmental interactions identified: rs1799964/C (TNF-α), rs769178/T (TNF-β), rs2189480/T (VDR), rs3782905/C (VDR), rs4890785/T (MBP), and rs7412/T (APOE).	N/A	25137520	Details
TPH2	SNP	rs4570625– rs10506645 GT	N/A	MS	Disease risk	The haplotype rs4570625-rs10506645TT of TPH2 gene was associated with the risk of severe disability in primary progressive MS(PPMS), while haplotype rs4570625-rs10506645TC appeared to be protective against disability in secondary progressive MS (SPMS).	in melatonin biosynthesis pathway	22698518	Details
VDR	allel	rs1540339/T	N/A	MS	Phenotypic risk	For mercury, there were four statistically significant environmental interactions: rs1540339/T (VDR), rs2189480/T (VDR), rs2239186/G (VDR), and rs8096433/A (MBP).	N/A	25137520	Details
TPH2	SNP	rs4570625– rs10506645 TC	N/A	MS	Disease risk	The haplotype rs4570625-rs10506645TT of TPH2 gene was associated with the risk of severe disability in primary progressive MS(PPMS), while haplotype rs4570625-rs10506645TC appeared to be protective against disability in secondary progressive MS (SPMS).	in melatonin biosynthesis pathway	22698518	Details
VDR	allel	rs2239186/G	N/A	MS	Phenotypic risk	For mercury, there were four statistically significant environmental interactions: rs1540339/T (VDR), rs2189480/T (VDR), rs2239186/G (VDR), and rs8096433/A (MBP).	N/A	25137520	Details
MTNR1B	SNP	rs10830963– rs4753426 CT	N/A	MS	Disease risk	In the MTNR1B gene, the haplotype rs10830963-rs4753426GC was associated with the risk of SPMS, whereas another haplotype rs10830963-rs4753426GT showed an association with the risk of PPMS.	membrane receptor gene (Melatonin receptor 1B, MTNR1B) essential for the function of melatonin	22698518	Details
VDR	allel	rs2238136/T	N/A	MS	Phenotypic risk	For mercury, there were four statistically significant environmental interactions: rs1540339/T (VDR), rs2189480/T (VDR), rs2239186/G (VDR), and rs8096433/A (MBP).	N/A	25137520	Details
MTNR1B	SNP	rs10830963– rs4753426 GC	N/A	MS	Disease risk	In the MTNR1B gene, the haplotype rs10830963-rs4753426GC was associated with the risk of SPMS, whereas another haplotype rs10830963-rs4753426GT showed an association with the risk of PPMS.	membrane receptor gene (Melatonin receptor 1B, MTNR1B) essential for the function of melatonin	22698518	Details
MBP	allel	rs8096433/A	N/A	MS	Phenotypic risk	Three statistically significant environmental interactions were also identified with reported exposure to solvents: rs2238136/T (VDR), rs8096433/A (MBP), and rs17660901/G (MBP).	N/A	25137520	Details
MTNR1B	SNP	rs10830963– rs4753426 CC	N/A	MS	Disease risk	In the MTNR1B gene, the haplotype rs10830963-rs4753426GC was associated with the risk of SPMS, whereas another haplotype rs10830963-rs4753426GT showed an association with the risk of PPMS.	membrane receptor gene (Melatonin receptor 1B, MTNR1B) essential for the function of melatonin	22698518	Details
MBP	allel	rs17660901/G	N/A	MS	Phenotypic risk	Three statistically significant environmental interactions were also identified with reported exposure to solvents: rs2238136/T (VDR), rs8096433/A (MBP), and rs17660901/G (MBP).	N/A	25137520	Details
CLEC16A	SNP	rs725613	N/A	MS	Disease risk	In these Sardinian samples, allele A of rs725613 is positively associated with MS .	CLEC16A belongs to the C-type lectin family and is expressed in immune cells.	18946483	Details
MTNR1B	SNP	rs10830963– rs4753426 GT	N/A	MS	Disease risk	In the MTNR1B gene, the haplotype rs10830963-rs4753426GC was associated with the risk of SPMS, whereas another haplotype rs10830963-rs4753426GT showed an association with the risk of PPMS.	membrane receptor gene (Melatonin receptor 1B, MTNR1B) essential for the function of melatonin	22698518	Details
VDR	allel	rs2189480/T	N/A	MS	Phenotypic risk	Three statistically significant environmental interactions were also identified with reported exposure to solvents: rs2238136/T (VDR), rs8096433/A (MBP), and rs17660901/G (MBP).	N/A	25137520	Details
IFNL3	SNP	rs8099917	N/A	MS	Treatment risk	Combined analysis of the study cohorts showed no significant associations between SNP rs8099917 and the response to treatment.	The IL28B gene codes for IFN-lambda 3 (IFN-λ-3), a cytokine induced by viral infections that is related with the type I IFNs and the IL-10 family.	21889215	Details
MBP	allel	rs8096433/A	N/A	MS	Phenotypic risk	For mercury, there were four statistically significant environmental interactions: rs1540339/T (VDR), rs2189480/T (VDR), rs2239186/G (VDR), and rs8096433/A (MBP).	N/A	25137520	Details
IFNL3	SNP	rs12979860	N/A	MS	Treatment risk	Combined analysis of the study cohorts showed no significant associations between SNP rs12979860 and the response to treatment.	The IL28B gene codes for IFN-lambda 3 (IFN-λ-3), a cytokine induced by viral infections that is related with the type I IFNs and the IL-10 family.	21889215	Details
IL7R	allel	rs6897932/A	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
TNF	allel	rs800629/A	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
TNF	allel	rs3093671/A	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
LTA	allel	rs769177/T	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
LTA	allel	rs909253/A	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
HLA-DRB1	allel	rs3135388/T	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
TRB	allel	rs17133575/G	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
HERV-K18	polymorphisms	SU	N/A	MS	Disease risk	It did not trigger phenotypic changes in a mouse model of experimental autoimmune encephalomyelitis.	N/A	35955468	Details
TRB	allel	rs17243/G	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
IL2RA	allel	rs2104286/C	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
NAT1	SNP	rs7388368	N/A	MS	Disease risk	Tobacco smoke exposure was associated with MS risk among rs7388368A carriers only	N/A	24625537	Details
VDR	allel	rs7975128/A	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
NAT1	SNP	rs4921877	N/A	MS	Disease risk	Tobacco smoke exposure was associated with MS risk among rs7388368A carriers only	N/A	24625537	Details
VDR	allel	rs2248098/A	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
TRB	rearrangement	N/A	N/A	MS	Disease risk	These results demonstrate that distinct oligoclonal T cell populations can be found in the CSF immune compartment of subjects with nonmalignant inflammatory disease and they can create a new avenue for the investigation of the specificity of the T cell response within the central nervous system.	N/A	3258624	Details
NAT1	SNP	rs6586711	N/A	MS	Disease risk	Tobacco smoke exposure was associated with MS risk among rs7388368A carriers only	N/A	24625537	Details
VDR	allel	rs2239182/T	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
VDR	allel	rs2107301/A	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
VDR	allel	rs2239179/C	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
TNF	polymorphism	TNF*(-308)A	N/A	MS	Disease risk	Thus, data obtained indicate the participation of TNF gene in MS susceptibility in Russians.	N/A	21090238	Details
VDR	allel	rs3819545/G	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
IFNG	polymorphism	TNF*(-308)A	N/A	MS	Disease risk	Linkage/association of IFNG and IL-6 alleles with MS was not revealed.	N/A	21090238	Details
VDR	allel	rs2228570/T	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
IL6	polymorphism	TNF*(-308)A	N/A	MS	Disease risk	Linkage/association of IFNG and IL-6 alleles with MS was not revealed.	N/A	21090238	Details
VDR	allel	rs2254210/A	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
GAL	SNP	rs948854	N/A	MS	Disease risk	An increase in the proportion of patients with a MSSS > 5 (high rate of progression) was observed among the minor G allele carriers (genotypes AG and GG) compared to patients with AA genotype.	one of the non-immune genes that may affect progression of multiple sclerosis.	32173003	Details
VDR	allel	rs2853564/G	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
VDR	allel	rs4760648/T	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
ST8SIA1	SNP	rs704219	N/A	MS	Disease risk	No significant association was found in the entire sample or when stratifying by transmitting parent, indicating that this gene plays little or no role in susceptibility to MS in the Canadian population.	N/A	19428123	Details
VDR	allel	rs11168287/G	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
ST8SIA1	SNP	rs2041906	N/A	MS	Disease risk	No significant association was found in the entire sample or when stratifying by transmitting parent, indicating that this gene plays little or no role in susceptibility to MS in the Canadian population.	N/A	19428123	Details
VDR	allel	rs4328262/G	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
ST8SIA1	SNP	rs1558793	N/A	MS	Disease risk	No significant association was found in the entire sample or when stratifying by transmitting parent, indicating that this gene plays little or no role in susceptibility to MS in the Canadian population.	N/A	19428123	Details
HLA-DPB1	polymorphism	DR2(+), DC 2.2(+)	N/A	MS	Disease risk	phenotype DR2(+), DC 2.2(-) is significantly more frequent in MS but not different in IDD.	N/A	6324215	Details
VDR	allel	rs4237855/G	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
ST8SIA1	SNP	rs4762896	N/A	MS	Disease risk	No significant association was found in the entire sample or when stratifying by transmitting parent, indicating that this gene plays little or no role in susceptibility to MS in the Canadian population.	N/A	19428123	Details
HLA-DPB1	polymorphism	DR2(+), DC 2.2(-)	N/A	MS	Disease risk	phenotype DR2(+), DC 2.2(-) is significantly more frequent in MS but not different in IDD.	N/A	6324215	Details
VDR	allel	rs7136534/T	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
H2	polymorphism	H-2s	N/A	EAE	Disease risk	SJL/J and SWR/J, which are H-2 s and H-2 q, respectively, are susceptible to EAE and sensitive to Bordetella pertussis histamine-sensitizing factor (HSF), which produces a vasoactive amine hypersensitivity.	N/A	6806429	Details
VDR	allel	rs7299460/A	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
H2	polymorphism	H-2q	N/A	EAE	Disease risk	SJL/J and SWR/J, which are H-2 s and H-2 q, respectively, are susceptible to EAE and sensitive to Bordetella pertussis histamine-sensitizing factor (HSF), which produces a vasoactive amine hypersensitivity.	N/A	6806429	Details
VDR	allel	rs4760658/G	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
H2-Ab1	polymorphism	H2-ABp	N/A	EAE	Disease risk	Our results suggest that the disease severity, but possibly not onset or disease type, is associated with the Ab-chain.	N/A	11694316	Details
VDR	allel	rs4516035/C	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
Ptpn6	Deletion	me+/-	N/A	EAE	Disease risk	mev-/- mice had a higher incidence of disease and developed a more severe course of EAE.	SHP-1 is a cytosolic tyrosine phosphatase that is involved in regulating the T cell activation cascade from signals initiated through the TCR.SHP-1-deficient mice have severe defects in immunity and hemopoiesis.	11970996	Details
H2-Ab1	polymorphism	H2-ABq	N/A	EAE	Disease risk	Our results suggest that the disease severity, but possibly not onset or disease type, is associated with the Ab-chain.	N/A	11694316	Details
MBP	allel	rs17026/C	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
HLA-DRB1	polymorphism	HLA-DRB1*15:01	N/A	MS	Disease risk	A higher HLAGB was associated with younger age at onset and the atrophy of subcortical gray matter fraction in women with relapsing-onset MS (standard β = 1.20 × 101; P = 1.7 × 102 and standard β = 1.67 × 101; P = 2.3 × 104, respectively), which were driven mainly by the HLA-DRB1*15:01 haplotype.	N/A	27244296	Details
MBP	allel	rs470724/T	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
HLA-A	polymorphism	HLA-A*02:01	N/A	MS	Disease risk	Association of HLA Alleles With MS.	N/A	27244296	Details
MBP	allel	rs470550/T	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
PRNP	SNP	Prnp129 M/V	N/A	MS	Disease risk	There was no statistically significant difference in frequency of Prnp129 genotypes between patients with PPMS and controls (P =.14)	N/A	21320996	Details
Tcrb	polymorphisms	Va	N/A	EAE	Disease risk	Thus, TCR Va2VB8.2 and its junctional region gene products are not the only prerequisite segment for a T cell to become encephalitogenic.	N/A	1714476	Details
HLA-B	polymorphism	HLA-B*38:01	N/A	MS	Disease risk	Association of HLA Alleles With MS.	N/A	27244296	Details
MBP	allel	rs9676113/G	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
PRNP	SNP	Prnp129 M/V	N/A	MS	Disease risk	There was also no difference in allelic frequency distributions between the 498 patients with PPMS and 979 patients with relapsing-remitting MS (P=.23)	N/A	21320996	Details
Tcrb	polymorphisms	Vb8.2	N/A	EAE	Disease risk	Thus, TCR Va2VB8.2 and its junctional region gene products are not the only prerequisite segment for a T cell to become encephalitogenic.	N/A	1714476	Details
HLA-B	polymorphism	HLA-B*44:02	N/A	MS	Disease risk	Association of HLA Alleles With MS.	N/A	27244296	Details
MBP	allel	rs11661054/A	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
VEGFA	genotype	rs1413711(T/T)	N/A	MS	Disease risk	The distribution of VEGFA rs1413711 genotypes (T/T, T/C, C/C) was statistically significantly different in the ON without MS group compared to the control.	A VEGFA role in MS development and overall in CNS inflammation when contributing together with adhesive molecules.	33121296	Details
HLA-B	polymorphism	rs9277565 (T)d	N/A	MS	Disease risk	Association of HLA Alleles With MS.	N/A	27244296	Details
MBP	allel	rs11661755/A	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
VEGFA	genotype	rs1413711(T/C)	N/A	MS	Disease risk	The distribution of VEGFA rs1413711 genotypes (T/T, T/C, C/C) was statistically significantly different in the ON without MS group compared to the control.	A VEGFA role in MS development and overall in CNS inflammation when contributing together with adhesive molecules.	33121296	Details
HLA-DRB1	polymorphism	HLA-DRB1*03:01	N/A	MS	Disease risk	Association of HLA Alleles With MS.	N/A	27244296	Details
MBP	allel	rs9675994/T	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
VEGFA	genotype	rs1413711(C/C)	N/A	MS	Disease risk	The distribution of VEGFA rs1413711 genotypes (T/T, T/C, C/C) was statistically significantly different in the ON without MS group compared to the control.	A VEGFA role in MS development and overall in CNS inflammation when contributing together with adhesive molecules.	33121296	Details
HLA-B	polymorphism	HLA-B*55:01	N/A	MS	Disease risk	Association of HLA Alleles With MS.	N/A	27244296	Details
MBP	allel	rs8090438/T	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
TIMP3	genotype	rs9621532(A/A)	N/A	MS	Disease risk	Our results showed that the IL-6 rs1800796, TIMP-3 rs9621532, and IL-6 rs1800796 were not associated with ON with MS development.	However, there are good insights into the role of proteases in neuroinflammation.	33121296	Details
HLA-DRB1	polymorphism	HLA-DRB1*13:03	N/A	MS	Disease risk	Association of HLA Alleles With MS.	N/A	27244296	Details
MBP	allel	rs8094402/G	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
TIMP3	genotype	rs9621532(C/C)	N/A	MS	Disease risk	Our results showed that the IL-6 rs1800796, TIMP-3 rs9621532, and IL-6 rs1800796 were not associated with ON with MS development.	However, there are good insights into the role of proteases in neuroinflammation.	33121296	Details
HLA-DQB1	polymorphism	HLA-DQB1*03:02	N/A	MS	Disease risk	Association of HLA Alleles With MS.	N/A	27244296	Details
MBP	allel	rs12456341/G	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
TIMP3	genotype	rs9621532(A/C)	N/A	MS	Disease risk	Our results showed that the IL-6 rs1800796, TIMP-3 rs9621532, and IL-6 rs1800796 were not associated with ON with MS development.	However, there are good insights into the role of proteases in neuroinflammation.	33121296	Details
HLA-DRB1	polymorphism	HLA-DRB1*08:01	N/A	MS	Disease risk	Association of HLA Alleles With MS.	N/A	27244296	Details
MBP	allel	rs17576751/T	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
IL6	genotype	rs1800796(C/G)	N/A	MS	Disease risk	Our results showed that the IL-6 rs1800796, TIMP-3 rs9621532, and IL-6 rs1800796 were not associated with ON with MS development.	IL-6 tends to shift the RGCs towards regenerative phenotype after damage to the optic nerve.	33121296	Details
HLA-DRB1	polymorphisms	HLA-DRB1*15:01	N/A	MS	Disease risk	Carriers of the HLADRB1*15:01 allele were significantly more common among the MS patients than in the group of healthy controls.When the subjects were divided according to sex, the frequency of the HLA-DRB1*15:01 carrier state was significantly higher among MS patients than among healthy subjects, both in females and in males (P = 0·0084 and P = 0·0058).	N/A	23379431	Details
MBP	allel	rs3794848/A	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
IL6	genotype	rs1800796(G/G)	N/A	MS	Disease risk	Our results showed that the IL-6 rs1800796, TIMP-3 rs9621532, and IL-6 rs1800796 were not associated with ON with MS development.	IL-6 tends to shift the RGCs towards regenerative phenotype after damage to the optic nerve.	33121296	Details
CHRNA9	SNP	rs6812832	N/A	MS	Disease risk	The results suggest that CHRNA7 and CHRNA9 modifies MS risk conferred by tobacco smoke, where risk among smokers was increased in carriers of the minor CHRNA9 haplotype and in non carriers the minor CHRNA7 haplotype.	N/A	32924781	Details
MBP	allel	rs4890875/G	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
IL6	genotype	rs1800796(C/C)	N/A	MS	Disease risk	Our results showed that the IL-6 rs1800796, TIMP-3 rs9621532, and IL-6 rs1800796 were not associated with ON with MS development.	IL-6 tends to shift the RGCs towards regenerative phenotype after damage to the optic nerve.	33121296	Details
CHRNA9	SNP	rs7681304	N/A	MS	Disease risk	The results suggest that CHRNA7 and CHRNA9 modifies MS risk conferred by tobacco smoke, where risk among smokers was increased in carriers of the minor CHRNA9 haplotype and in non carriers the minor CHRNA7 haplotype.	N/A	32924781	Details
MBP	allel	rs595997/G	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
HLA-DRB1	polymorphisms	DRB1*0101	N/A	MS	Disease risk	Carriage frequencies of HLA-DRB1 alleles in MS vs controls by 2-digit and 4-digit HLA genotyping	N/A	20207784	Details
CHRNA9	SNP	rs4861307	N/A	MS	Disease risk	The results suggest that CHRNA7 and CHRNA9 modifies MS risk conferred by tobacco smoke, where risk among smokers was increased in carriers of the minor CHRNA9 haplotype and in non carriers the minor CHRNA7 haplotype.	N/A	32924781	Details
MBP	allel	rs2974260/T	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
HLA-DRB1	polymorphisms	DRB1*0102	N/A	MS	Disease risk	Carriage frequencies of HLA-DRB1 alleles in MS vs controls by 2-digit and 4-digit HLA genotyping	N/A	20207784	Details
HLA-DRB1	SNP	rs2076530	N/A	MS	N/A	However, despite adequate power to detect an independent association, no difference in transmission of BTNL2 alleles or genotypes was observed in DRB1*15-negative individuals with MS.	N/A	16321988	Details
CHRNA7	SNP	rs11635209	N/A	MS	Disease risk	The results suggest that CHRNA7 and CHRNA9 modifies MS risk conferred by tobacco smoke, where risk among smokers was increased in carriers of the minor CHRNA9 haplotype and in non carriers the minor CHRNA7 haplotype.	N/A	32924781	Details
MBP	allel	rs2051344/A	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
HLA-DRB1	polymorphisms	DRB1*0103	N/A	MS	Disease risk	Carriage frequencies of HLA-DRB1 alleles in MS vs controls by 2-digit and 4-digit HLA genotyping	N/A	20207784	Details
CHRNA7	SNP	rs35114543	N/A	MS	Disease risk	The results suggest that CHRNA7 and CHRNA9 modifies MS risk conferred by tobacco smoke, where risk among smokers was increased in carriers of the minor CHRNA9 haplotype and in non carriers the minor CHRNA7 haplotype.	N/A	32924781	Details
MBP	allel	rs470681/C	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
HLA-DRB1	polymorphisms	DRB1*0301	N/A	MS	Disease risk	Carriage frequencies of HLA-DRB1 alleles in MS vs controls by 2-digit and 4-digit HLA genotyping	N/A	20207784	Details
CHRNA7	SNP	rs2175886	N/A	MS	Disease risk	The results suggest that CHRNA7 and CHRNA9 modifies MS risk conferred by tobacco smoke, where risk among smokers was increased in carriers of the minor CHRNA9 haplotype and in non carriers the minor CHRNA7 haplotype.	N/A	32924781	Details
MBP	allel	rs12967023/A	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
HLA-DRB1	polymorphisms	DRB1*0401	N/A	MS	Disease risk	In addition we found evidence that the DRB1*04 sub-allele HLA-DRB1*0407 and HLA-DRB1*0901 may be protective.	N/A	20207784	Details
CHRNA7	SNP	rs1604265	N/A	MS	Disease risk	The results suggest that CHRNA7 and CHRNA9 modifies MS risk conferred by tobacco smoke, where risk among smokers was increased in carriers of the minor CHRNA9 haplotype and in non carriers the minor CHRNA7 haplotype.	N/A	32924781	Details
MBP	allel	rs4890788/T	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
HLA-DRB1	polymorphisms	DRB1*0402	N/A	MS	Disease risk	In addition we found evidence that the DRB1*04 sub-allele HLA-DRB1*0407 and HLA-DRB1*0901 may be protective.	N/A	20207784	Details
CHRNA7	SNP	rs8033518	N/A	MS	Disease risk	The results suggest that CHRNA7 and CHRNA9 modifies MS risk conferred by tobacco smoke, where risk among smokers was increased in carriers of the minor CHRNA9 haplotype and in non carriers the minor CHRNA7 haplotype.	N/A	32924781	Details
MBP	allel	rs7232502/A	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
HLA-DRB1	polymorphisms	DRB1*0403	N/A	MS	Disease risk	In addition we found evidence that the DRB1*04 sub-allele HLA-DRB1*0407 and HLA-DRB1*0901 may be protective.	N/A	20207784	Details
CHRNA7	SNP	rs2133965	N/A	MS	Disease risk	The results suggest that CHRNA7 and CHRNA9 modifies MS risk conferred by tobacco smoke, where risk among smokers was increased in carriers of the minor CHRNA9 haplotype and in non carriers the minor CHRNA7 haplotype.	N/A	32924781	Details
APOE	allel	rs429358/C	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
HLA-DRB1	polymorphisms	DRB1*0404	N/A	MS	Disease risk	In addition we found evidence that the DRB1*04 sub-allele HLA-DRB1*0407 and HLA-DRB1*0901 may be protective.	N/A	20207784	Details
CHRNA7	SNP	rs6494212	N/A	MS	Disease risk	The results suggest that CHRNA7 and CHRNA9 modifies MS risk conferred by tobacco smoke, where risk among smokers was increased in carriers of the minor CHRNA9 haplotype and in non carriers the minor CHRNA7 haplotype.	N/A	32924781	Details
APOE	allel	rs7412/T	N/A	MS	Phenotypic risk	Associations between environmental exposures, SNPs, and MS case-control status adjusted for education and ancestry.	N/A	25137520	Details
HLA-DRB1	polymorphisms	DRB1*0405	N/A	MS	Disease risk	In addition to the known risk allele HLA-DRB1*1501, evidence of increased susceptibility to MS was found for three additional alleles, DRB1*0405, DRB1*1104 and DRB1*1303, though the power was insufficient to sustain significance for these when crudely Bonferroni corrected over all alleles considered.	N/A	20207784	Details
HLA-DRB1	polymorphisms	DRB1*0407	N/A	MS	Disease risk	Carriage frequencies of HLA-DRB1 alleles in MS vs controls by 2-digit and 4-digit HLA genotyping	N/A	20207784	Details
PLAT	insertion/deletion (I/D) genetic polymorphism	TPA DD/PAI-1 4G4G	N/A	MS	Disease risk	TPA DD/PAI-1 4G4G genotype combination has reached a borderline significance for reduced risk for MS	he explanation for this interaction may be a complex interplay between these two pleiotropic proteins within the brain tissue and in plasma.	17986506	Details
HLA-DQA1	polymorphisms	*0101	N/A	MS	Disease risk	DQA Gene Frequency Analysis of 116 Unrelated Patients With Multiple Sclerosis (MSU)* and 32 Related Patients With Multiple Sclerosis(MSR), 23 Parents (Pa) and 27 Siblings (Si) of Patients With MSR, and 86 Healthy Controls (C)	N/A	8442703	Details
HLA-DRB1	polymorphisms	DR1	N/A	MS	Disease risk	These differences were not significant when corrected for the number of antigens tested.	N/A	3492235	Details
HLA-DRB1	polymorphisms	DRB1*0701	N/A	MS	Disease risk	In addition to the known risk allele HLA-DRB1*1501, evidence of increased susceptibility to MS was found for three additional alleles, DRB1*0405, DRB1*1104 and DRB1*1303, though the power was insufficient to sustain significance for these when crudely Bonferroni corrected over all alleles considered.	N/A	20207784	Details
SERPINE1	insertion/deletion (I/D) genetic polymorphism	TPA DD/PAI-1 4G4G	N/A	MS	Disease risk	TPA DD/PAI-1 4G4G genotype combination has reached a borderline significance for reduced risk for MS	he explanation for this interaction may be a complex interplay between these two pleiotropic proteins within the brain tissue and in plasma.	17986506	Details
HLA-DQA1	polymorphisms	*0102	N/A	MS	Disease risk	TheDQA1 *0301 allele was found to be increased in patients, while the DQA1 *0102 allele was found to be diminished in patients with MSr vs controls(Pc=.001 ).	N/A	8442703	Details
HLA-DRB1	polymorphisms	DR2	N/A	MS	Disease risk	These differences were not significant when corrected for the number of antigens tested.	N/A	3492235	Details
HLA-DRB1	polymorphisms	DRB1*0801	N/A	MS	Disease risk	Carriage frequencies of HLA-DRB1 alleles in MS vs controls by 2-digit and 4-digit HLA genotyping	N/A	20207784	Details
HLA-DQA1	polymorphisms	*0103	N/A	MS	Disease risk	DQA Gene Frequency Analysis of 116 Unrelated Patients With Multiple Sclerosis (MSU)* and 32 Related Patients With Multiple Sclerosis(MSR), 23 Parents (Pa) and 27 Siblings (Si) of Patients With MSR, and 86 Healthy Controls (C)	N/A	8442703	Details
HLA-DRB1	polymorphisms	DR3	N/A	MS	Disease risk	These differences were not significant when corrected for the number of antigens tested.	N/A	3492235	Details
HLA-DRB1	polymorphisms	DRB1*0901	N/A	MS	Disease risk	In addition we found evidence that the DRB1*04 sub-allele HLA-DRB1*0407 and HLA-DRB1*0901 may be protective.	N/A	20207784	Details
HLA-DRB1	haplotypic diversity	HLA-DRB1*1501	N/A	MS	Disease risk	A selective association with HLA-DRB1*15 was revealed, indicating a primary role for the DRB1 locus in MS independent of DQB1*0602	a substantial proportion of the susceptibility chromosomes from African American patients with MS displayed haplotypes consistent with an African origin.	14669136	Details
HLA-DQA1	polymorphisms	*0201	N/A	MS	Disease risk	DQA Gene Frequency Analysis of 116 Unrelated Patients With Multiple Sclerosis (MSU)* and 32 Related Patients With Multiple Sclerosis(MSR), 23 Parents (Pa) and 27 Siblings (Si) of Patients With MSR, and 86 Healthy Controls (C)	N/A	8442703	Details
HLA-DRB1	polymorphisms	DR4	N/A	MS	Disease risk	These differences were not significant when corrected for the number of antigens tested.	N/A	3492235	Details
HLA-DRB1	polymorphisms	DRB1*1001	N/A	MS	Disease risk	Carriage frequencies of HLA-DRB1 alleles in MS vs controls by 2-digit and 4-digit HLA genotyping	N/A	20207784	Details
HLA-DQB1	haplotypic diversity	HLA-DQB1*0602	N/A	MS	Disease risk	A selective association with HLA-DRB1*15 was revealed, indicating a primary role for the DRB1 locus in MS independent of DQB1*0602	a substantial proportion of the susceptibility chromosomes from African American patients with MS displayed haplotypes consistent with an African origin.	14669136	Details
HLA-DQA1	polymorphisms	*0301	N/A	MS	Disease risk	TheDQA1 *0301 allele was found to be increased in patients, while the DQA1 *0102 allele was found to be diminished in patients with MSr vs controls(Pc=.001 ).	N/A	8442703	Details
HLA-DRB1	polymorphisms	DR5	N/A	MS	Disease risk	These differences were not significant when corrected for the number of antigens tested.	N/A	3492235	Details
HLA-DRB1	polymorphisms	DRB1*1101	N/A	MS	Disease risk	Carriage frequencies of HLA-DRB1 alleles in MS vs controls by 2-digit and 4-digit HLA genotyping	N/A	20207784	Details
C4A	allele	C4AQ0(null allele at the C4A locus)	N/A	MS	Disease risk	On excess of C4AQ0 homozygosity was observed in MS patients compared to controls.This gene may favour the occurrence of MS and accelerate the evolution and severity of the disease.	A deleted or intact C4 gene, present but not expressed, provokes an altered immune response to viral and/or bacterial aggression, with a decrease in immune clearance.This gene may favour the occurrence of MS and accelerate the evolution and severity of the disease.	2089531	Details
HLA-DQA1	polymorphisms	*0401	N/A	MS	Disease risk	DQA Gene Frequency Analysis of 116 Unrelated Patients With Multiple Sclerosis (MSU)* and 32 Related Patients With Multiple Sclerosis(MSR), 23 Parents (Pa) and 27 Siblings (Si) of Patients With MSR, and 86 Healthy Controls (C)	N/A	8442703	Details
HLA-DRB1	polymorphisms	DRw6	N/A	MS	Disease risk	These differences were not significant when corrected for the number of antigens tested.	N/A	3492235	Details
HLA-DRB1	polymorphisms	DRB1*1103	N/A	MS	Disease risk	Carriage frequencies of HLA-DRB1 alleles in MS vs controls by 2-digit and 4-digit HLA genotyping	N/A	20207784	Details
HLA-DQA1	polymorphisms	*0501	N/A	MS	Disease risk	DQA Gene Frequency Analysis of 116 Unrelated Patients With Multiple Sclerosis (MSU)* and 32 Related Patients With Multiple Sclerosis(MSR), 23 Parents (Pa) and 27 Siblings (Si) of Patients With MSR, and 86 Healthy Controls (C)	N/A	8442703	Details
HLA-DRB1	polymorphisms	DR7	N/A	MS	Disease risk	These differences were not significant when corrected for the number of antigens tested.	N/A	3492235	Details
HLA-DRB1	polymorphisms	DRB1*1104	N/A	MS	Disease risk	In addition to the known risk allele HLA-DRB1*1501, evidence of increased susceptibility to MS was found for three additional alleles, DRB1*0405, DRB1*1104 and DRB1*1303, though the power was insufficient to sustain significance for these when crudely Bonferroni corrected over all alleles considered.	N/A	20207784	Details
HLA-DRB1	Alleles	NA	NA	MS	Disease risk	However, the presence of different HLA class II allele associations, such as DRB1*1501 (DR2) in Caucasians (Hillert and Olerup 1993) and DRB1*040.. (DR4) and DRB1 *0301 (DR3), demonstrated both elsewhere (Marrosu et al. 1988) and in this report, suggests the possibility that any of these alleles may be the locus primarily involved in susceptibility to MS.	The inheritance of MS appears to be complex and is believed to involve several genes	9311753	Details
MAMU-DPB	allele	Mamu-DPB1*01	nucleotide sequencing or oligotyping	EAE	Disease risk	In the group of animals that developed EAE, nine out of 15 animals were positive for the Mamu-DPB1*01 allele, whereas all eight non-susceptible animals lacked this allele.	N/A	8562513	Details
HLA-G	SNP	—725C>G>T	PCR and DNA sequencing	MS	Disease risk	ignificant differences were found only for the -725 promoter SNP. The -725C allele was significantly less frequent in the MS patients than in the controls, whereas the -725G allele was significantly more frequent in the MS patients than in the healthy subjects	It is possible that the association of HLA-G with MS observed in our study is due to a strong linkage disequilibrium	20636826	Details
HLA-G	SNP	—716>G>T	PCR and DNA sequencing	MS	Disease risk	For the second promoter SNP, we observed a non-significant but clearly higher percentage of -716TGheterozygotes in the controls than in all patients andin those with the relapsing–remitting form of the dis-ease	It is possible that the association of HLA-G with MS observed in our study is due to a strong linkage disequilibrium	20636826	Details
HLA-G	indel	N/A	PCR and DNA sequencing	MS	Disease risk	We observed a strong trend for association of 14bpindel polymorphism with ADO	It is possible that the association of HLA-G with MS observed in our study is due to a strong linkage disequilibrium	20636826	Details
HLA-DRB1	SNP	DRB1*1501	PCR and sequence-specific oligonucleotide probes	MS	Disease risk	the DR2-associated DRB1*1501 allele and DRB5*0101 allele were associated with Western-type MS (41.2%), but not with either Asian-type MS (0%) or healthy control subjects (14.2%)	suggests the importance of the DRB 1 *1501 molecule in the genera- tion of autoaggressive T cells against myelin	8871575	Details
HLA-DRB5	SNP	DRB5*0101	PCR and sequence-specific oligonucleotide probes	MS	Disease risk	the DR2-associated DRB1*1501 allele and DRB5*0101 allele were associated with Western-type MS (41.2%), but not with either Asian-type MS (0%) or healthy control subjects (14.2%)	This finding supports a critical role of immunogenetic background in the development and manifestations of MS	8871575	Details
IL2	polymorphisms	The positionβ384 in the promoter region	PCR – RFLP	MS	Disease risk	Our results showed no significant differences in the distribution of the two polymorphisms between MS patients and controls. Furthermore,no association was observed between IL-2 gene polymorphisms and clinical characteristics	no functional significance	12409183	Details
IL2	polymorphisms	The position +114 in the first exon	PCR – RFLP	MS	Disease risk	Our results showed no significant differences in the distribution of the two polymorphisms between MS patients and controls. Furthermore,no association was observed between IL-2 gene polymorphisms and clinical characteristics	no functional significance	12409183	Details
HLA-DRB1	allele	DRB1*1501-positive and -negative	PCR followed by restriction fragment length polymorphisms techniques	MS	Disease risk	The comparison between HLA DRB1*1501-positive and - negative MS patients did not show significant differences for age, gender, age at disease onset and clinical MS subtype. No significant effect of HLA DRB1*1501 status was found on clinical (Extended Disability Status Scale, MS Severity Score (MSSS)) and cognitive (SDMT) disabilities.	N/A	21179117	Details
HLA-B	allele	HLA B*44	PCR followed by restriction fragment length polymorphisms techniques	MS	Disease risk	HLA B*44 also have consistent effects on MRI parameters in the entire MS population. Subjects carrying HLA B*44 were also significantly associated with better performance on Symbol Digit Modalities Test (SDMT).	HLA B*44 has been shown to modulate the immune response.	21179117	Details
HLA-DRB1	allele	DRB1*0301	PCR sequence-specific primer method	MS	Disease risk	HLA class II analyses Case–control analysis was significant for the HLA-DRB1 gene in both the Muslim and the Christian populations.Further analysis indicated that in the Muslim population, DRB1*0301 is a major susceptibility allele, positively associated to MS.Surprisingly, in the Christian Arab population the DRB1*0301 allele was negatively associated with MS. Moreover, DRB1*0301 homozygotes were observed only in the Christian control group.	Multiple sclerosis (MS) is a neurological disease with a strong inflammatory component.The major genetic effect has been attributed to the 6p major histocompatibility complex region, comprising the human leukocyte antigen (HLA) genes.	20463743	Details
HLA-DQB1	allele	DQB1*0201	PCR sequence-specific primer method	MS	Disease risk	Analysis of the DQB1 locus revealed a significant difference between cases and controls in the Muslim, and trend for the Christian population.Positive association of the HLA-DQB1*0201 allele in Muslims, and negative association in Christian Arabs.	Multiple sclerosis (MS) is a neurological disease with a strong inflammatory component.The major genetic effect has been attributed to the 6p major histocompatibility complex region, comprising the human leukocyte antigen (HLA) genes.	20463743	Details
HLA-B	allele	HLA-B*52	PCR sequence-specific primer method	MS	Disease risk	The HLA-B*52 allele remained significant after correcting for multiple testing, was negatively associated with MS and totally absent from the patient population.	Multiple sclerosis (MS) is a neurological disease with a strong inflammatory component.The major genetic effect has been attributed to the 6p major histocompatibility complex region, comprising the human leukocyte antigen (HLA) genes.	20463743	Details
MAG	SNP	N/A	PCR,DHPLC	MS	N/A	Considering the statistical power of the experimental design, these results exclude the MAG gene as an MS susceptibility factor with an odds ratio (OR) equal or higher than 1.3.	N/A	12020971	Details
NOS2	SNP	Exon 10 C/T	PCR,microsatellite markers	MS	Disease risk	A significant increase in frequency of the less common NOS2A exon10 SNP-T allele was observed.	The NOS2A locus encodes one of the three isoforms of nitric oxide (NO) synthase, inducible NOS2 oriNOS, and is a very plausible MS candidate gene based on the well-known biological functions attributed to this enzyme.	15174013	Details
IL32	SNP	rs45499297	PCR,RFLP analysis	MS	Disease risk	The presence of C allele might impact the risk of disease susceptibility up to 1.6 fold. Harboring CC genotype significantly increased IL-32 levels in both groups .ANOVA revealed a significance difference between age at disease onset and IL-32 T/C genotypes .Tukey’s Post Hoc test was shown a significant decreased in age at disease onset in CC genotype compared to CT genotype. C allele carriage patients were significantly younger than the T allele carrier patients .Comparison of MS symptoms in wild IL-32 genotype carriages with mutant C allele harboring subjects revealed no significant difference.	N/A	28716229	Details
TRBV20OR9-2	allele	N/A	PCR,Southern blot hybridizations	MS	Disease risk	Genotypes in the normal populations were compared to those in the MS population .The genotype frequencies were not significantly different between the MS and control populations at positions 1-4 and 6 (Vβ7/BamHI and Vβ15/MSP 1 markers, Vβ1/TaqI and Vβ8/MSP 1 markers ,Vβ8/BamHI.) However, at marker 5 defined by the Vβ11/BarnHI RFLP, the genotype frequencies were significantly different between the MS and control populations.These subhaplotype frequency distributions were not significantly different among the control populations.The subhaplotype frequency distributions spanning the markers * 4 and * 5 were found to be significantly different between the MS and control population .	N/A	8101191	Details
TRBV20OR9-2	allele	N/A	PCR,Southern blot hybridizations	MS	Disease risk	The Vβ8/BamHI-Vβ11/BamHI subhaplotype frequencies differed significantly only in the HLA-DR2 + MS patients but not in the HLA-DR2- MS patients.	N/A	8101191	Details
FTO	SNP	rs9939609	PCR,TaqMan	MS	Disease risk	After adjustment for potential confounders, the risk-associated FTO rs9939609 A-allele was associated with raised homocysteine levels (p = 0.003) in patients diagnosed with MS, but not in controls.	N/A	24532085	Details
IL2RA	SNP	rs2104286	PCR,TaqMan	MS	Disease risk	Replication and meta-analysis with results from an independent cohort of 771 MS patients and 759 controls from Andalucía (Spain) confirmed the association of polymorphisms in the IL2RA gene (P(Mantel-Haenszel,) odds ratio (OR)(M-H) (95% confidence interval, CI) for rs2104286: 0.0001, 0.75 (0.65-0.87); for rs11594656/rs35285258: 0.004, 1.19 (1.06-1.34); for rs41295061: 0.03, 0.77 (0.60-0.98))	The relevant role of the IL2RA gene on MS susceptibility adds support to its common effect on autoimmune risk and the suggestive association of IL2/IL21 warrants further investigation.	20179739	Details
IL2RA	SNP	rs11594656	PCR,TaqMan	MS	Disease risk	Replication and meta-analysis with results from an independent cohort of 771 MS patients and 759 controls from Andalucía (Spain) confirmed the association of polymorphisms in the IL2RA gene (P(Mantel-Haenszel,) odds ratio (OR)(M-H) (95% confidence interval, CI) for rs2104286: 0.0001, 0.75 (0.65-0.87); for rs11594656/rs35285258: 0.004, 1.19 (1.06-1.34); for rs41295061: 0.03, 0.77 (0.60-0.98))	The relevant role of the IL2RA gene on MS susceptibility adds support to its common effect on autoimmune risk and the suggestive association of IL2/IL21 warrants further investigation.	20179739	Details
HLA-DRB1	SNP	rs3135388	PCR,TaqMan	MS	Disease risk	We found significantly higher frequency of rs3135388 A allele carriers in MS patients compared to controls.	N/A	19433080	Details
CNR2	SNP	rs35761398	PCR,TaqMan	MS	Disease risk	The co-dominant, dominant, recessive, over-dominant, and additive inheritance models were analyzed using SNPStats software. A significant genetic association was observed between Q63R polymorphism and MS. The dominant model was accepted as the best inheritance model to fit the data (OR 2.70, 95% CI 1.47-4.97, p = 0.001).	N/A	31407233	Details
GTF2I	SNP	rs117026326	PCR,TaqMan	MS	N/A	The rs117026326 variant does not affect the risk for MS.	N/A	31520790	Details
MTHFR	polymorphism	C677T	PCR-based restriction fragment length polymorphism assay	MS	Disease risk	The genotype and allele frequencies of C677T polymorphism showed statistically significant differences between MS patients and controls.A significant association was observed when the patients were compared with the controls according to CC genotype versus CT + TT genotypes.	MTHFR is a key enzyme-regulating folate and homocysteine metabolism.The MTHFR enzyme catalyzes the irreversibly conversion of methylenetetrahydrofolate (5,10-MTHF) to 5- methyltetrahydrofolate (5-MTHF).In homocysteine metabolism, 5-MTHF is necessary to remethylate the neurotoxic intermediate homocysteine to methionine, which itself serves as precursor of S-adenosylmethionine (SAM), essential for CNS myelination. The MTHFR C677T polymorphism leads to mild hyperhomocysteinemia and impairs the ability to process folate and methionine.Elevated homocysteine levels and reduced availability of SAM can increase the risk of extensive neuronal loss combined with diffuse demyelination.Moreover, homocysteine can directly damage CNS cells or influence macrophage activation, both of which are important aspects of MS pathology.	25203152	Details
HLA-G	SNP	rs1611715	PCR-HRM	MS	Disease risk	In this research, we found significantly different distribution of HLA-G polymorphism between MS patients and healthy individuals.	Multiple sclerosis (MS) is the most common chronic inflammatory demyelinating disorder of central nervous system in young population. It has been suggested that major histocompatibility complex (MHC) on chromosome 6p21 is the strongest genome-wide MS susceptibility factor. HLA-G is a non-classical HLA class I with limited polymorphisms.	29924453	Details
IL27	polymorphism	N/A	PCR-restriction fragment length polymorphism analysis	MS	Disease risk	Carriers of the T4730С polymorphism were found to have a 6-fold increased risk for MS. Univariate logistic regression analysis showed an increased frequency of the TC4730 heterozygous genotype and also of the C4730 allele in patients compared to controls, with a 6.02-fold increased risk and a 4.31-fold increased risk of developing MS.	IL27 is a novel member of the IL12 family, known for both its pro- and anti-inflammatory functions, with distinct roles in shaping the activity of T-cells. IL27 regulates the immune response through its heterodimeric IL27Ra/GP130 receptor, activating multiple signaling cascades.In the brain, IL27 produced by astrocytes and microglial cells is recognized for its neuroprotective effects, enhancing the production of nerve growth factor and neurotrophic factor, promoting remyelination.	34410977	Details
IFNG	SNP	IFN-γ intron III (+2118 site A/G and +3586 site G/ACT).	PCR-RFL	MS	Disease risk	The frequency of the A allele at the IFN-γ +2118 site was increased in the MS group as compared with the control group.However, no significant difference was observed between the MS and control groups in genotype distribution and allele frequency at the IFN-γ +3586 site.Thus, polymorphisms at the +2118 A/G site in the IFN-γ intron III gene may be associated with susceptibility to multiple sclerosis.	Interferon-gamma (IFN-γ), which is a pro-inflammatory cytokine secreted by Th1 cells, can regulate the activity of immune cells and induce general inflammation. Studies have shown that level of IFN-γ increases in the acute phase of MS. IFN-γ may therefore act as a direct inducer of demyelination in the central nervous system.	28218775	Details
CYP27B1	Gene polymorphisms	genotype bb	PCR-RFLP	MS	Disease risk	In MS patients, genotype bb was significantly higher than the healthy controls	Binding of vitamin D to its specific nuclear receptors is a way to exert its function	32914731	Details
NGF	SNP	rs6330	PCR-RFLP	MS	Disease risk	rs6330 showed significant association in allele (p = 0.0038; OR = 1.210 (1.063–1.377)) and genotype frequencies (p = 0.0126) when comparing healthy controls and MS patients	Nerve growth factor β (NGFB) is involved in cell proliferation and survival, and it is a mediator of the immune response	19063739	Details
NGF	SNP	rs11102930	PCR-RFLP	MS	Disease risk	23 male MS patients were characterized via quantitative RT-PCR after selection for opposite homozygosity in rs11102930: No correlation was observed between genotypes and expression levels	Nerve growth factor β (NGFB) is involved in cell proliferation and survival, and it is a mediator of the immune response	19063739	Details
IL7R	SNP	rs11567685	PCR-RFLP	MS	Disease risk	In addition, whereas no association was found between the alternative splicing SNP, rs6897932, and MS, a significant link was found between the promoter SNP, rs11567685, and MS.	N/A	24166352	Details
NGF	SNP	rs7523831	PCR-RFLP	MS	Disease risk	Subsequent genotyping of three flanking SNPs (rs6327, rs7523831 and rs11102915) in subgroups of our cohorts of 263 rr MS patients and 259 controls showed no additional significant association	Nerve growth factor β (NGFB) is involved in cell proliferation and survival, and it is a mediator of the immune response	19063739	Details
IL7R	SNP	rs6897932	PCR-RFLP	MS	N/A	In addition, whereas no association was found between the alternative splicing SNP, rs6897932, and MS, a significant link was found between the promoter SNP, rs11567685, and MS.	N/A	24166352	Details
NGF	SNP	rs11102915	PCR-RFLP	MS	Disease risk	Subsequent genotyping of three flanking SNPs (rs6327, rs7523831 and rs11102915) in subgroups of our cohorts of 263 rr MS patients and 259 controls showed no additional significant association	Nerve growth factor β (NGFB) is involved in cell proliferation and survival, and it is a mediator of the immune response	19063739	Details
NGF	SNP	rs6327	PCR-RFLP	MS	Disease risk	Subsequent genotyping of three flanking SNPs (rs6327, rs7523831 and rs11102915) in subgroups of our cohorts of 263 rr MS patients and 259 controls showed no additional significant association	Nerve growth factor β (NGFB) is involved in cell proliferation and survival, and it is a mediator of the immune response	19063739	Details
NGF	SNP	rs2239622	PCR-RFLP	MS	Disease risk	No significant association was found for SNPs rs2239622 and rs910330 flanking exon 2 in the subgroups of our cohorts	Nerve growth factor β (NGFB) is involved in cell proliferation and survival, and it is a mediator of the immune response	19063739	Details
NGF	SNP	rs910330	PCR-RFLP	MS	Disease risk	No significant association was found for SNPs rs2239622 and rs910330 flanking exon 2 in the subgroups of our cohorts	Nerve growth factor β (NGFB) is involved in cell proliferation and survival, and it is a mediator of the immune response	19063739	Details
HSPA4	gene polymorphism	hsp70 -2 (+1267 A/G)	PCR-RFLP	MS	Disease risk	indicating animplication of the G allele ofHSP70-2 gene polymorphism in the development ofMS.	an inducible chaperon induced under stress conditions	24485944	Details
NGF	SNP	rs3811014	PCR-RFLP	MS	Disease risk	Analyses of three flanking SNPs, rs3811014, rs17540656 and rs6673867 in the defined subgroups showed no significant association for male MS patients compared to healthy male controls as well as no significant association between female MS patients and female controls	Nerve growth factor β (NGFB) is involved in cell proliferation and survival, and it is a mediator of the immune response	19063739	Details
NGF	SNP	rs17540656	PCR-RFLP	MS	Disease risk	Analyses of three flanking SNPs, rs3811014, rs17540656 and rs6673867 in the defined subgroups showed no significant association for male MS patients compared to healthy male controls as well as no significant association between female MS patients and female controls	Nerve growth factor β (NGFB) is involved in cell proliferation and survival, and it is a mediator of the immune response	19063739	Details
CD24	SNP	N/A	PCR-RFLP	MS	Disease risk	A comparison of genotype frequencies between MS patients and controls indicates that the CD24v/v genotype was significantly more frequent in MS patients than in controls.The results showed a significant difference in the MSSS of the three different genotypes.These data suggest that the CD24v/v genotype may influence both disease susceptibility and severity in Iranian MS patients.	CD24 is one of the non-HLA genes suggested to contribute to the pathogenesis of MS. It is a glycosylphosphatidylinositol (GPI)-linked cell surface glycoprotein expressed in a broad range of hematopoietic system cells, including T cells, B cells, macrophages, and neutrophils.It ′is also known that CD24 is abundantly expressed in CNS cells such as astrocytes and microglia.CD24 contributes to the pathogenesis of MS through several mechanisms, including expansion of autoreactive T cells in the target organ and regulation of homeostatic proliferation.	21815873	Details
NGF	SNP	rs6673867	PCR-RFLP	MS	Disease risk	Analyses of three flanking SNPs, rs3811014, rs17540656 and rs6673867 in the defined subgroups showed no significant association for male MS patients compared to healthy male controls as well as no significant association between female MS patients and female controls	Nerve growth factor β (NGFB) is involved in cell proliferation and survival, and it is a mediator of the immune response	19063739	Details
VDR	polymorphism	TaqI, ApaI	PCR-RFLP	MS	Disease risk	No association was found between VDR variants and MS, but they were shown to moderately modulate the risk conferred by *15:01.	N/A	22127897	Details
UCP2	SNP	rs660339	PCR-RFLP	MS	Disease risk	Our results confirm the link between UCP2 SNP and MS, and show a slight relation between this SNP and mitochondrial haplogroups.	N/A	17463068	Details
PVR	polymorphism	N/A	PCR-RFLP	MS	Disease risk	We did not find a significant difference in the frequency of the four polymorphisms in the PVR gene between MS patients and controls.	PVR mediates entry of neurotropic viruses to the brain.Functional PVR, called the bona fide receptor, is essential for entry of the polio virus in neurons. In the CNS, both receptors are structural CNS proteins and important for cellular interactions.	15465608	Details
APOE	allele	N/A	PCR-RFLP	MS	Disease risk	We did not find a difference between patients and controls with respect to the ApoE4 allele.	N/A	15465608	Details
TNF	polymorphism	376a	PCR-RFLP	MS	Disease risk	No significant differences in genotype and allele frequencies were found between groups of healthy individuals and patients with MS.	N/A	18051225	Details
ARSA	polymorphism	ASA-PD (N350S and 1524+95A-G)	PCR-RFLP	MS	Phenotypic risk	Comparison of MR findings between MS patients, mutations carrier vs. non-carrier, matched for sex, age and disease duration, showed that the total number of lesions and the number of hypointense lesions on T1-weighted images was greater in MS patient carrying the ASA-PD mutations.	Different levels of enzyme deficiency, due to mutations in ASA gene, could lead to long-term accumulation of non-degraded substrate and thus influence the cellular vulnerability. In multiple sclerosis, the same mechanism could underlie a death of oligodendrocyte subpopulations thus enabling liberation of myelin antigens and stimulation of immune response.	21648305	Details
VDR	SNP	rs2228570	PCR-RFLP	MS	Disease risk	There were no significant differences in the polymorphism of FokI (rs2228570) in VDR gene among patients and controls	The role of vitamin D receptor (VDR) gene and its polymorphisms are highlighted as susceptible components	25854779	Details
VDR	SNP	rs1544410	PCR-RFLP	MS	Disease risk	while a significant difference was observed in BsmI (rs1544410) polymorphism in healthy subjects and homozygous genotype-b/b- with MS	The role of vitamin D receptor (VDR) gene and its polymorphisms are highlighted as susceptible components	25854779	Details
TNF	polymorphisms	(-308)	PCR-RFLP	MS	Disease risk	No differences in the distribution of the TNF-a )238 and )308 alleles were observed.	N/A	20082645	Details
TNF	polymorphisms	(-238)	PCR-RFLP	MS	Disease risk	No differences in the distribution of the TNF-a )238 and )308 alleles were observed.	N/A	20082645	Details
TNF	polymorphisms	(-857)	PCR-RFLP	MS	Disease risk	We observed a statistically significant increase in TNF-a 857 CC genotype in MS patients than controls (P < 0.001) while TNF-a 857 CT genotype showed a significant negative correlation with MS patients (P = 0.033).	N/A	20082645	Details
VDR	SNP	rs2228570	PCR-RFLP	MS	Disease risk	Our results suggest that FokI and TaqI polymorphisms ofVDR are associated with MS risk and TaqI polymorphism is associated with Vitamin D levels in MS patients. Meanwhile, no difference was observed between VDR gene polymorphisms and any types of MS.	preventing inflammatory disorders	33485603	Details
VDR	SNP	rs1544410	PCR-RFLP	MS	Disease risk	Our results suggest that FokI and TaqI polymorphisms ofVDR are associated with MS risk and TaqI polymorphism is associated with Vitamin D levels in MS patients. Meanwhile, no difference was observed between VDR gene polymorphisms and any types of MS.	preventing inflammatory disorders	33485603	Details
VDR	SNP	rs731236	PCR-RFLP	MS	Disease risk	Our results suggest that FokI and TaqI polymorphisms ofVDR are associated with MS risk and TaqI polymorphism is associated with Vitamin D levels in MS patients. Meanwhile, no difference was observed between VDR gene polymorphisms and any types of MS.	preventing inflammatory disorders	33485603	Details
CD24	allele	CD24 V/V	PCR-RFLP	MS	Disease risk	Our results confirm the association between the V/V genotype at aa 57 of this gene and MS and highlight the importance of taking into account the origin of the subjects to avoid a population bias.	N/A	16900767	Details
TNF	polymorphism	TNF-α 376	PCR-RFLP	MS	Disease risk	We could not detect the AA homozygote genotype in either the MS patients or the HC.For the GG genotype, a statistically significant higher level was found in the PPMS group as compared with the HC group.As regards the G allele, a significant difference was observed between the PPMS and HC groups. The GA genotype was underrepresented in the PPMS group relative to the HC group; for the A allele, the distribution was similar.	Tumour necrosis factor (TNF) is a proinflammatory cytokine involved in the pathogenesis of infectious and autoimmune disorders, including MS. TNF causes apoptotic cell death, cellular proliferation, differentiation, inflammation and tumourgenesis.	19201038	Details
TNF	SNP	rs1800629	PCR-RFLP	MS	Disease risk	The differences in genotype distribution were observed after stratification by gender.The female patients showed a significantly elevated frequency of heterozygotes lsthose carrying at least one A-allele (GA/AA genotype) in comparison with the healthy women.In opposite, the distribution of genotypes in men was similar in the group of patients and controls.The frequency of heterozygote GA-genotype was overrepresented among RRMS women with early-onset compared with healthy women.Also, in women with an early manifestation of RRMS, the frequency of A-allele was significantly higher and the wild GG-genotype was less frequent compared with the women of the control group.The distribution of genotype in male patients with early and late-onset of RRMS was lower than healthy men without reaching statistical significance.Moreover, the carriers of at least one A-allele of -308G/A TNF-α polymorphism (GA+AA) are significantly associated with two fold increased risk for RRMS development in women in contrast to men as well as associated with early onset of the disease.	Tumor necrosis factor-alpha (TNF-α) is a potent pro-inflammatory cytokine with a pleiotropic effect,involved in acute and systemic inflammation.TNF-α interacts with two cell-surface TNF receptors–TNFR1 (55kDa) and TNFR2 (75 kDa) and triggers the cell survival and pro-inflammatory NF-kB and MAP kinases activation.	33252003	Details
IL-12B	SNP	rs3212227	PCR-RFLP	MS	Disease risk	Our study showed that the IL-12B and IL23R gene SNPs does not seem to be associated with MS susceptibility in Chinese southern population.	N/A	24547735	Details
IL-23R	SNP	rs2201841	PCR-RFLP	MS	Disease risk	Our study showed that the IL-12B and IL23R gene SNPs does not seem to be associated with MS susceptibility in Chinese southern population.	N/A	24547735	Details
IL-23R	SNP	rs10889677	PCR-RFLP	MS	Disease risk	Our study showed that the IL-12B and IL23R gene SNPs does not seem to be associated with MS susceptibility in Chinese southern population.	N/A	24547735	Details
NFKB1	Gene polymorphisms	-94 ins/del ATTG promoter polymorphism	PCR-RFLP	MS	Disease risk	our study showed no association between -94 ins/del ATTG polymorphism and risk of multiple sclerosis in Iranian patients	NF-κB1 is one of the most important molecules which regulates the immune functions	23618653	Details
IL-23R	SNP	rs7517847	PCR-RFLP	MS	Disease risk	Our study showed that the IL-12B and IL23R gene SNPs does not seem to be associated with MS susceptibility in Chinese southern population.	N/A	24547735	Details
GSTP1	polymorphism	A313 G	PCR-RFLP	MS	Disease risk	Comparison of the genotype distribution between MS cases and controls revealed no significant differences.Allele frequencies distribution analysis showed similar A and G allele frequencies for both MS patients and controls.	Germline polymorphisms of detoxification genes could influence susceptibility to Multiple Sclerosis (MS).Glutathione-S-transferases (GSTs) is detoxifying enzymes involved in biotransformation of metabolites preventing cells from oxidative damage.	24588223	Details
GSTP1	polymorphism	A313 G	PCR-RFLP	MS	Phenotypic risk	Regarding classification of patients in clinical subtypes, a higher variant G allele frequency was observed in RR patients, as compared to the controls. A significantly higher frequency of heterozygotes A/G was observed in RR patients as compared to the control population. The patients with EDSS ≤ 2 and a benign clinical course exhibit 1.5-fold increased risk of carrying the heterozygous variant genotype, as compared to the patients with EDSS>2 .	Germline polymorphisms of detoxification genes could influence susceptibility to Multiple Sclerosis (MS).Glutathione-S-transferases (GSTs) is detoxifying enzymes involved in biotransformation of metabolites preventing cells from oxidative damage.	24588223	Details
APOE	allele	N/A	PCR-RFLP	MS	Disease risk	It seems that individuals carrying APOE-ε4 allele and/or APOE-ε3ε4 genotype develop MS two times more than non-carriers.Also APOE-ε2ε3 genotype or APOE-ε2 allele may have a protective role against MS development in Iranian population.	The APOE gene consists of four exons and produces ApoE which is a 299 amino acid polypeptide.These different amino acids alter the protein's structure and influence its lipid association and receptor binding. ApoE is synthesized predominantly by astrocytes in the nervous system and delivers cholesterol and other essential lipids to neurons through members of the low density lipoprotein receptor family. This process is important in remodeling and repair of nerve tissue.ApoE also has immunomodulatory properties and plays an important role in modifying brain inflammatory responses.	22698480	Details
MTHFR	SNP	rs1801133	PCR-RFLP	MS	Disease risk	There were no differences in distribution of genotypes for the MTR A[66]G and MTR A[2756]C polymorphisms between patients with MS and controls (p > 0.05). Our findings suggested that the MTHFR C[677]T and MTHFR A[1298]C gene polymorphisms might be associated with MS as genetic factors influencing the risk of the disease	Methylenetetrahydrofolate reductase (MTHFR), methionine synthase (MTR) and methionine synthase reductase (MTRR) are essential enzymes in folate and Hcy metabolism, also in methylation reactions which provide a methyl group for conversion of homocysteine into methionine. MTHFR converts 5,10-methylenetetrahydrofolate, in a reaction catalysed by MTR	31038186	Details
MTHFR	SNP	rs1801131	PCR-RFLP	MS	Disease risk	There were no differences in distribution of genotypes for the MTR A[66]G and MTR A[2756]C polymorphisms between patients with MS and controls (p > 0.05). Our findings suggested that the MTHFR C[677]T and MTHFR A[1298]C gene polymorphisms might be associated with MS as genetic factors influencing the risk of the disease	Methylenetetrahydrofolate reductase (MTHFR), methionine synthase (MTR) and methionine synthase reductase (MTRR) are essential enzymes in folate and Hcy metabolism, also in methylation reactions which provide a methyl group for conversion of homocysteine into methionine. MTHFR converts 5,10-methylenetetrahydrofolate, in a reaction catalysed by MTR	31038186	Details
MTHFR	SNP	rs1805087	PCR-RFLP	MS	Disease risk	There were no differences in distribution of genotypes for the MTR A[66]G and MTR A[2756]C polymorphisms between patients with MS and controls (p > 0.05). Our findings suggested that the MTHFR C[677]T and MTHFR A[1298]C gene polymorphisms might be associated with MS as genetic factors influencing the risk of the disease	Methylenetetrahydrofolate reductase (MTHFR), methionine synthase (MTR) and methionine synthase reductase (MTRR) are essential enzymes in folate and Hcy metabolism, also in methylation reactions which provide a methyl group for conversion of homocysteine into methionine. MTHFR converts 5,10-methylenetetrahydrofolate, in a reaction catalysed by MTR	31038186	Details
MTHFR	SNP	rs1801394	PCR-RFLP	MS	Disease risk	There were no differences in distribution of genotypes for the MTR A[66]G and MTR A[2756]C polymorphisms between patients with MS and controls (p > 0.05). Our findings suggested that the MTHFR C[677]T and MTHFR A[1298]C gene polymorphisms might be associated with MS as genetic factors influencing the risk of the disease	Methylenetetrahydrofolate reductase (MTHFR), methionine synthase (MTR) and methionine synthase reductase (MTRR) are essential enzymes in folate and Hcy metabolism, also in methylation reactions which provide a methyl group for conversion of homocysteine into methionine. MTHFR converts 5,10-methylenetetrahydrofolate, in a reaction catalysed by MTR	31038186	Details
LTA	allele	TNF-β +252	PCR-RFLP	MS	Disease risk	Allelic and genotypic frequencies for this polymorphism was similar in patients with MS and population controls or among different types of the disease. The mentioned functional polymorphism is not likely to cause susceptibility to MS in the Iranian population.	Pro-inflammatory cytokines, such as tumor necrosis factor-b (TNF-b), has a detrimental role in MS induction.	17295710	Details
IL4	allele	IL-4 (-590)	PCR-RFLP	MS	Disease risk	Allelic and genotypic frequencies for this polymorphism was similar in patients with MS and population controls or among different types of the disease. The mentioned functional polymorphism is not likely to cause susceptibility to MS in the Iranian population.	The anti-inflammatory cytokines, such as interleukin-4 (IL-4), has a beneficial role in preventing lesion formation or relapse of the disease.	17295710	Details
PTAFR	polymorphism	A224D	PCR-RFLP	MS	Disease risk	The frequency of the AD/DD genotypes was significantly higher in MS patients than in healthy controls.Moreover, the frequency of D allele in MS patients was also significantly higher than those in healthy controls.	PAF is a very potent chemotactic stimulant for inflammatory cells such as eosinophils and polymorphonuclear neutrophils. PAF not only promotes leukocyte adhesion and transmigration by the induction of intracellular adhesion molecule-1 (ICAM-1) on endothelial cells, but also upregulates major histocompatibility complex (MHC) class I and II expressions in some brain cells thatare critical in antigen presentation.These proinflammatory and vasoactive actions of PAF are mediated through a specific G-protein-coupled receptor, PAFR .	15748960	Details
TNF	Gene polymorphisms	TNF-alpha - 238 G-->A	PCR-RFLP	MS	Disease risk	The genotypes and allele frequencies were not different between patient and control groups	N/A	11571703	Details
TNF	Gene polymorphisms	TNF-alpha - 308 G-->A	PCR-RFLP	MS	Disease risk	The genotypes and allele frequencies were not different between patient and control groups	N/A	11571703	Details
VDR	SNP	rs731236	PCR-RFLP	MS	Disease risk	The frequency of C allele of TaqI polymorphism was significantly higher in patients than in controls (P values < 0.0001; OR = 18.9, 95% CI in 11.6–30.3); it can be concluded that allele C showed positive association and allele T showed negative association with MS.	Although we could not yet definitely emphasize the role of polymorphisms on VDR function, consider that the variation in vitamin D receptor may affect the ligandreceptor affinity or signaling pathway or gene expression and so indirectly affect the function of vitamin D.	25685788	Details
VDR	SNP	rs7975232	PCR-RFLP	MS	Disease risk	In the ApaI single nucleotide polymorphism investigation (rs7975232), homozygote genotype CC was significantly higher in patients (P = 0.036; OR = 3.4, 95% CI in 1.1–10.4) in comparison to controls. However, the AA genotype frequency indicated negative associations with MS too.	Although we could not yet definitely emphasize the role of polymorphisms on VDR function, consider that the variation in vitamin D receptor may affect the ligandreceptor affinity or signaling pathway or gene expression and so indirectly affect the function of vitamin D.	25685788	Details
TNF	SNP	rs1800629 G/A	PCR-RFLP	MS	Disease risk	The TNF-α-308 AA genotype and A allele could be related to disability progression and severity of MS and the IL-18-607 AA genotype A allele could be related to susceptibility of the disease in the Egyptian cohort.	N/A	33302229	Details
FOXP3	SNP	rs3761548	PCR-RFLP	MS	Disease risk	The A allele was significantly more frequent in MS patients than controls.The C allele for rs3761548 was significantly higher in controls than patients.The association between recessive model of rs3761548 with MS remained significant the results are summarized in. According to the co-dominant model the A/A and C/C homozygote genotype frequencies of rs3761548 were significantly different between patients and controls and they respectively conferred susceptibility and protection toward MS in the study group.	The commitment stage of Treg cell differentiation, the continued gene expression of FOXP3 gene in CD4+CD25+T lymphocytes is needed as a Treg cell lineage specification factor to direct developing thymocytes towards the Treg cell lineage, Taken together, these studies suggest that dysfunction and aberrant expression of the FOXP3 gene underlie different immune diseases.	27792007	Details
IL18	SNP	rs1946518 C/A	PCR-RFLP	MS	Disease risk	The TNF-α-308 AA genotype and A allele could be related to disability progression and severity of MS and the IL-18-607 AA genotype A allele could be related to susceptibility of the disease in the Egyptian cohort.	N/A	33302229	Details
FOXP3	SNP	rs2232365	PCR-RFLP	MS	Disease risk	The A allele was significantly more frequent in MS patients than controls.The G allele for rs2232365 was significantly higher in controls than patients.The association between recessive model of rs2232365 with MS remained significant the results are summarized in. A similar significant negative and positive trend for MS disease was observed for the A/A and G/G homozygote genotype frequencies of rs2232365. Neither the A/C or the A/G heterozygote genotypes were statistically significant.	The commitment stage of Treg cell differentiation, the continued gene expression of FOXP3 gene in CD4+CD25+T lymphocytes is needed as a Treg cell lineage specification factor to direct developing thymocytes towards the Treg cell lineage, Taken together, these studies suggest that dysfunction and aberrant expression of the FOXP3 gene underlie different immune diseases.	27792007	Details
IL16	SNP	rs4072111 C/T	PCR-RFLP	MS	N/A	The IL-16 (rs4072111 C/T) polymorphism was not polymorphic in both MS patients and the healthy volunteers.	N/A	33302229	Details
MMP9	SNP	rs3918242	PCR-RFLP	MS	Disease risk	In conclusion, MMP9 genotypes of rs3918242 have a role in MS susceptibility, but not with severity	MMP-9 (which represents the largest and most complex of MMP family) was a subject for functional polymorphism of rs3918242 gene	31082619	Details
IL2	allele	IL2 -330 GT , TT ,GG	PCR-RFLP	MS	Disease risk	The higher expression of IL2 -330 GT and TT genotypes, associated with susceptibility to MS, and the altered relative expression between alleles in MS patients supports the importance of IL2 in the MS.	Importance of IL-2/IL-2R system for the T cell homeostasis at the levels of repertoire selection, the generation of suppressive regulatory T cells, T cell homing and clonal contraction via activation induced cell death indicates its relevance in the development of autoimmune disease.	14975604	Details
TNFSF10	SNP	1595C/T	PCR-RFLP	MS	Disease risk	The presence of the CC genotype at position 1595 in exon 5 represents a higher risk of MS.	N/A	16040132	Details
FOXO3	SNP	rs2253310	PCR-RFLP	MS	Disease risk	In addition, it has been determined that variants of FOXO3a (rs2253310, rs4966936) and FOXO1 (rs3900833), which have been genotyped, may be effective in disease pathogenesis.	N/A	31759981	Details
FOXO3	SNP	rs4966936	PCR-RFLP	MS	Disease risk	In addition, it has been determined that variants of FOXO3a (rs2253310, rs4966936) and FOXO1 (rs3900833), which have been genotyped, may be effective in disease pathogenesis.	N/A	31759981	Details
IL16	SNP	rs4072111	PCR-RFLP	MS	Disease risk	The IL-16 rs4072111C/T genotype and allele frequencies showed significantly differences between MS patients and controls.The genotype frequencies of the rs4072111C/T were 62% CC, 30.8% CT, and 7.2% TT in MS patients and were 79% CC, 18% CT, and 3% TT in the control groups.Allele frequencies of C and T alleles were 77.4% and 22.6% for MS patients, and 88% and 12% for control subjects, respectively.	Interleukin-16 (IL-16), a pleiotropic cytokine, is an important regulator of T-cell activation which plays a key role in autoimmune diseases. Single-nucleotide polymorphisms (SNPs) in the IL-16 gene may lead to altered cytokine expression or biological activity, and these variations may modulate an individual’s risk for MS.	28151028	Details
FOXO1	SNP	rs3900833	PCR-RFLP	MS	Disease risk	In addition, it has been determined that variants of FOXO3a (rs2253310, rs4966936) and FOXO1 (rs3900833), which have been genotyped, may be effective in disease pathogenesis.	N/A	31759981	Details
IL16	SNP	rs11556218	PCR-RFLP	MS	Disease risk	Statistically significant differences were also found in allele and genotype frequencies of rs11556218 G/T between two groups.In MS patients, the genotype frequencies of rs11556218T/G were 32.8% for TT, 59.2% for TG, and 8% for GG and were 54% for TT, 42% for TG, and 4% for GG in healthy controls.Allele frequencies of T and G alleles were 62.4% and 37.6% for MS patients, and 75% and 25% for control subjects, respectively.	Interleukin-16 (IL-16), a pleiotropic cytokine, is an important regulator of T-cell activation which plays a key role in autoimmune diseases. Single-nucleotide polymorphisms (SNPs) in the IL-16 gene may lead to altered cytokine expression or biological activity, and these variations may modulate an individual’s risk for MS.	28151028	Details
IL7R	SNP	rs6897932	PCR-RFLP	MS	Disease risk	In our study, there were no significant differences in genotype frequencies in the IL-7RA rs6897932 polymorphism and no significant difference between C and T alleles in patients with MS and controls.	An enormous amount of research has shown that immune mediators such as cytokines and chemokines are the culprits of MS pathophysiology.There are several lines of evidence indicating that the receptor of interleukin (IL)-7 is associated with the risk of MS. The IL-7 receptor (IL-7R) gene is located on the short arm of chromosome 5 at position 13 (5p13), consisting of a γ-chain (IL7Rγ) and an α-chain (IL7-RA).As the T244I variant of the IL-7RA gene,rs6897932 is considered to be the strongest single-nucleotide polymorphism (SNP) associated with MS.	33354118	Details
IL25	polymorphisms	c424C/A	PCR-RFLP	MS	Disease risk	The results showed that there was no statistical significant difference in distribution of genotype (AA, AC and CC) and allele (A and C) frequencies between MS patients and healthy controls .	This cytokine has a similar structure to IL-17 and plays a key role in stimulating and development of T helper 2 (Th2) responses.Furthermore, IL-25 is involved in the control function of endothelial cell, Th1 and Th17, which are the main cells involved in the pathogenic activities of the immune system. Therefore, any factor, which can regulate the expression of the cytokine, can be considered as a candidate for investigation in the MS disease process.	28144453	Details
VEGFA	SNP	rs3025039	PCR-RFLP	MS	Disease risk	VEGF 936C > T showed an association with patients in a recessive model	VEGF and KDR pathway trigger the process of angiogenesis as well as inflammation, which contributes to the development and progression of demyelinating lesions in multiple sclerosis	28401369	Details
KDR	SNP	rs2071559	PCR-RFLP	MS	Disease risk	the KDR -604T > C (rs2071559) polymorphism showed no significant difference in either allelic or genotype frequency between the two groups	VEGF and KDR pathway trigger the process of angiogenesis as well as inflammation, which contributes to the development and progression of demyelinating lesions in multiple sclerosis	28401369	Details
NOS3	SNP	rs1799983	PCR-RFLP	MS	Disease risk	Statistical analysis showed that according to co-dominant model, c.894G>T polymorphism is associated with risk of MS.The prevalence of T allele was significantly higher in patients compared to the control group.	Multiple Sclerosis (MS) is a neuroimmunological disease, causing severe neurological disabilities as a result of demyelination.An important role for Nitric Oxide (NO) in the pathogenesis of MS and its influence on the various aspects of the disorder, including changes in synaptic transmission, inflammation, and neuronal death were pointed by abundant evidence.An isoform of NO producing enzymes is endothelial Nitric Oxide Synthase (NOS3) that is constitutively expressed in endothelial cells.This enzyme has been found to play a prominent role in both vasculogenesis and angiogenesis.There are two common polymorphisms of NOS3 gene in many populations that are associated with NOS3 enzyme activity and production.	29158878	Details
PDCD1	SNP	rs36084323	PCR-RFLP	MS	Disease risk	The frequency difference of PD-1.1 genotypes and alleles (-536 G/A) between patients and healthy controls was not significant.	Programmed cell death 1 (PD-1) is an immune checkpoint and has been reported to be associated with several autoimmune diseases.	36308011	Details
PDCD1	SNP	rs11568821	PCR-RFLP	MS	Disease risk	Regarding PD-1.3, the AA + AG genotype was found to be relatively higher in the control group.	Programmed cell death 1 (PD-1) is an immune checkpoint and has been reported to be associated with several autoimmune diseases.	36308011	Details
PDCD1	SNP	rs2227981	PCR-RFLP	MS	Disease risk	Concerning PD-1.5 (+7785 C/T), the frequency of T allele carriers (TT + CT) was relatively higher in MS patients, which was marginally insignificant .	Programmed cell death 1 (PD-1) is an immune checkpoint and has been reported to be associated with several autoimmune diseases.	36308011	Details
FOXP3	SNP	rs2232369	PCR-RFLP	MS	Disease risk	When the allele frequencies found in MS patients and healthy controls were compared, no significant difference of distribution was observed between the two groups.	Recent studies have shown that FoxP3 (forhead boxP3-scurfin) transcription factor is important in realizing the regulatory function of Treg cells.SNP may change the amino acid encoded by the gene, may stay silent or may be present in the regions where encoding does not occur.Therefore, it may play a significant role in development of autoimmune diseases by affecting gene production, mRNA formation or protein production.	28360598	Details
IL7R	SNP	rs7718919	PCR-RFLP	MS	Disease risk	Significant association was gained while the subtype stratification was applied on genotype level: relapsing-remitting (RRMS) in SNP rs7718919.Based on gender Allelic frequency of SNP rs7718919 in the males which are affected by MS showed a significant association to disease.	Multiple sclerosis (MS) is a neurodegenerative disease in the central nervous system (CNS) that usually occurs in young adults.More than three decades after the apparition of susceptibility effect of HLA genes, the interleukin-7 receptor alpha chain (IL-7Ra) or (CD127) located on chromosome 5P13 was identified as the first non-major histocompatibility complex (non-MHC) MS susceptibility locus.IL-7Ra gene has crucial roles in some processes in the immune system such as development, maturation, and homeostasis of T and B cells.	26221483	Details
IL7R	SNP	rs11567685	PCR-RFLP	MS	Disease risk	Significant association was gained while the subtype stratification was applied on genotype level: for secondary-progressive multiple sclerosis (SPMS) in SNP rs11567685.Also allelic frequency of rs11567685 SNP showed a significant association for SPMS patients.Allelic analysis in the female group showed significant results for SPMS in SNP rs11567685 also this association was gained in the genotypic level of RR MS patients in the case of SNP rs11567685.	Multiple sclerosis (MS) is a neurodegenerative disease in the central nervous system (CNS) that usually occurs in young adults.More than three decades after the apparition of susceptibility effect of HLA genes, the interleukin-7 receptor alpha chain (IL-7Ra) or (CD127) located on chromosome 5P13 was identified as the first non-major histocompatibility complex (non-MHC) MS susceptibility locus.IL-7Ra gene has crucial roles in some processes in the immune system such as development, maturation, and homeostasis of T and B cells.	26221483	Details
RPS6KB1	SNP	rs180515	PCR-RFLP	MS	Disease risk	Our results showed significant difference in allelic frequency of SNP rs180515 among cases and controls (P = 0.004).	encodes p70S6K1 protein	28079472	Details
IL7R	SNP	rs6897932	PCR-RFLP	MS	Disease risk	Genotyping of SNP rs6897932 in SPMS of the male group demonstrated a significant statistical difference between cases.	Multiple sclerosis (MS) is a neurodegenerative disease in the central nervous system (CNS) that usually occurs in young adults.More than three decades after the apparition of susceptibility effect of HLA genes, the interleukin-7 receptor alpha chain (IL-7Ra) or (CD127) located on chromosome 5P13 was identified as the first non-major histocompatibility complex (non-MHC) MS susceptibility locus.IL-7Ra gene has crucial roles in some processes in the immune system such as development, maturation, and homeostasis of T and B cells.	26221483	Details
RPS6KB1	SNP	rs180515 AA	PCR-RFLP	MS	Disease risk	For this variation, AA genotype was shown to have protective effect (P = 0.016 and OR = 0.6), while GG genotype was a susceptive genotype to MS (P = 0.04 and OR = 2.2).	encodes p70S6K1 protein	28079472	Details
HSPA1A	SNP	rs1061581	PCR-RFLP	MS	Disease risk	Genotypic frequencies of HSP70 gene pointed to a non-significant association between polymorphism (AA/AG/GG) were observed at 0, genotype and presence of RRMS.We found no significant difference between RRMS patients and controls in the Iranian population based on the HSP70 variant.	HSP70 have two physiological neuroprotective roles.In specific, they act as molecular chaperones that assist the proper folding of newly synthesized proteins, preventing protein aggregation, and degrading unstable and misfolded proteins.HSP70 may also act as a cytokine by stimulating a pro-inflammatory signal transduction cascade in monocytes.It has been proposed that in MS patients, overexpression of HSP70 proteins can protect the CNS from inflammation so that the CNS can help towards myelin repair.	30124009	Details
RPS6KB1	SNP	rs180515 AG	PCR-RFLP	MS	Disease risk	For this variation, AA genotype was shown to have protective effect (P = 0.016 and OR = 0.6), while GG genotype was a susceptive genotype to MS (P = 0.04 and OR = 2.2).	encodes p70S6K1 protein	28079472	Details
IL7	SNP	rs1520333	PCR-RFLP	MS	Disease risk	The frequency of the C allele in cases was more than that in the healthy control group.A notable association of the allele G and the GG genotype of rs1520333 SNP was detected with higher MS risk.For other genotypes of the rs1520333 polymorphism, results were not significantly associated with the risk for MS in the population under study.	One of the new susceptibility genetic variants that have been introduced by a new GWAS is rs1520333 SNP in the IL-7 gene related to MS.The protein encoded by this gene is a cytokine that is secreted by stromal cells in the bone marrow and thymus.IL-7 cytokine plays an important role in immune system such as T-cell development, peripheral T-cell homeostasis, pre-B-cell growth factor and immune tolerance.MS usually has an autoimmune pathology in which TH1 and TH17 lymphocytes have a key contribution.In this pathology pathway, IL-7 cytokine directly elevated effector TH17 cells in human TH17 cells from subjects with MS;however, it is not necessary for TH17 differentiation.	25538924	Details
RPS6KB1	SNP	rs180515 GG	PCR-RFLP	MS	Disease risk	For this variation, AA genotype was shown to have protective effect (P = 0.016 and OR = 0.6), while GG genotype was a susceptive genotype to MS (P = 0.04 and OR = 2.2).	encodes p70S6K1 protein	28079472	Details
CD86	SNP	rs9282641	PCR-RFLP	MS	Disease risk	Allelic frequency of SNP rs9282641 also showed significant difference between cases and controls (P = 0.006).	CD86 gene codes a membrane protein type I	28079472	Details
CD86	SNP	rs9282641 GG	PCR-RFLP	MS	Disease risk	For this SNP, AG genotype had predisposing effect (P = 0.04, OR = 2.3), and GG genotype showed protective (P = 0.01, OR = 0.411).	CD86 gene codes a membrane protein type I	28079472	Details
CD86	SNP	rs9282641 AG	PCR-RFLP	MS	Disease risk	For this SNP, AG genotype had predisposing effect (P = 0.04, OR = 2.3), and GG genotype showed protective (P = 0.01, OR = 0.411).	CD86 gene codes a membrane protein type I	28079472	Details
CD86	SNP	rs9282641 AA	PCR-RFLP	MS	Disease risk	For this SNP, AG genotype had predisposing effect (P = 0.04, OR = 2.3), and GG genotype showed protective (P = 0.01, OR = 0.411).	CD86 gene codes a membrane protein type I	28079472	Details
DNMT3B	SNP	rs1569686	PCR-RFLP	MS	Disease risk	There was no statistically significant association between DNMT3B-579G>T and susceptibility to MS. The alleles and genotypes of DNMT3B-579G>T did not have different risks of MS development under various models.	Growing evidence about the relationship between methylation aberration or impaired DNMTs function and autoimmune diseases such as systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), Sjogren's syndrome (SS), MS, psoriasis, and autoimmune thyroid diseases (AITD).DNMT3B gene has been mapped on chromosome 20q11.2 and encodes a DNMT enzyme contributing mainly in de novo methylation. Single nucleotide polymorphisms (SNPs) in this gene could affect the potential of DNA methylation, gene expression, and consequently, the development of various diseases.	31565203	Details
MMP9	SNP	rs3918242	PCR-RFLP	MS	Disease risk	We detected a significant linkage/association between MS and MMP9 *(–1562)С alleles.	The matrix metalloproteinases (MMPs) play the key role in this barrier penetration.The MMPs are involved in various stages of MS pathogenesis: they participate in the local damaging of the hematoencephalic barrier and perivascular lymphocytes infiltration, in the damaging of myelin sheath and in the formation of the demyelination lesions and axonal death. One of the major metalloproteinases, MMP9, is expressed by perivascular mononuclear cells of white matter and, together with other MMPs, is associated with monocytes and astrocytes in the demyelination lesions.	22649676	Details
IL1B	Gene polymorphisms	allele 2 of the Taq1	PCR-RFLP	MS	Disease risk	Taq1 polymorphism in the IL-1beta gene and the variable number of tandem repeats (VNTR) polymorphism of 86-base pairs within the IL-1Ra gene cannot explain these findings	N/A	12020968	Details
IL1RN	Gene polymorphisms	allele 2 of VNTR locus	PCR-RFLP	MS	Disease risk	Taq1 polymorphism in the IL-1beta gene and the variable number of tandem repeats (VNTR) polymorphism of 86-base pairs within the IL-1Ra gene cannot explain these findings	N/A	12020968	Details
IL21	SNP	rs2055979	PCR-RFLP	MS	Disease risk	The results of the study revealed a significant reduction in the distribution of the wild homozygous genotype (GG) in MS patients, in comparison to a healthy control group.However, MS cases and controls did not differ significantly in neither GT nor TT genotypes,	B-cell proliferation is induced by IL-21, which improves their function by increasing antibody production and reducing cell death. It is also been linked to controlling antibody development and preventing apoptosis and plasma cell differentiation. The cluster of differentiation 81 T cells, NK cells, and NK T cells are activated by IL-21, which enhances their cytotoxic activity and proliferation.	35891764	Details
IL2	SNP	631 and 475 IL-2 promoter polymorphisms	PCR-RFLP	MS	Disease risk	We have found a low frequency of both SNPs and no differences between MS patient and control groups, it appears that these polymorphisms have no significant influence in MS susceptibility.	N/A	12358847	Details
MIF	SNP	rs755622	PCR-RFLP	MS	Disease risk	There was no statistically significant difference in allele and genotype frequencies between MS-patients and controls .No association was observed when the patients were compared against controls in terms of GG versus GC+CC genotypes and GG+GC versus CC genotypes .	N/A	25600533	Details
LEP	SNP	rs2167270 or 19G > A	PCR-RFLP	MS	Disease risk	The frequency of rs2167270 AG+AA (intermediate+high leptin producer genotypes) and rs2167270A (high leptin producer allele) was significantly higher in MS patients compared to those in controls.Further categorization of studied groups according to their gender showed a significant association between inheritance of intermediate+high leptin signaler genotypes and MS susceptibility in males.	MS is mainly considered a Th1-mediated inflammatory disease,although recent studies postulate a vital role for helper T cells-17 (Th17 cells) in the pathogenesis of the disease .Therefore, the pathogenesis of MS is influenced by factors that affect the deviation of nave CD4+ Th cells towards Th1 or Th17 cells.Among different factors, the effects of adipokines such as adiponectin and leptin on Th cell deviation have recently drawn much attention.	30219158	Details
FAS	SNP	a band at 189 bp (allele G) or a band at 233 bp (allele A)	PCR-RFLP	MS	Disease risk	We found no evidence that the polymorphism contributes to susceptibility to MS. Furthermore, there was no association between Apo-1/Fas gene polymorphisms and clinical course .No significant association was observed between Apo-1/Fas gene polymorphisms and the age at disease onset.	N/A	12188927	Details
LEP	SNP	rs7799039 or -2,548G > A	PCR-RFLP	MS	Disease risk	After classification of LEP rs7799039 genotypes to high (AA) and intermediate+low (AG+GG) leptin producers, it has been revealed that the frequency of high leptin producer genotype was significantly higher in male patients compared to male controls.	MS is mainly considered a Th1-mediated inflammatory disease,although recent studies postulate a vital role for helper T cells-17 (Th17 cells) in the pathogenesis of the disease .Therefore, the pathogenesis of MS is influenced by factors that affect the deviation of nave CD4+ Th cells towards Th1 or Th17 cells.Among different factors, the effects of adipokines such as adiponectin and leptin on Th cell deviation have recently drawn much attention.	30219158	Details
LEP	SNP	rs2167270 or 19G > A	PCR-RFLP	MS	Phenotypic risk	The results did not show any significant association between clinical parameters (including the EDSS score, progression index and the age of disease onset) and different studies genotypes of LEP gene polymorphisms. Also, there were no significant differences in the distributions of LEP rs2167270 genotypes in MS patients with different types of the disease .	MS is mainly considered a Th1-mediated inflammatory disease,although recent studies postulate a vital role for helper T cells-17 (Th17 cells) in the pathogenesis of the disease .Therefore, the pathogenesis of MS is influenced by factors that affect the deviation of nave CD4+ Th cells towards Th1 or Th17 cells.Among different factors, the effects of adipokines such as adiponectin and leptin on Th cell deviation have recently drawn much attention.	30219158	Details
LEP	SNP	rs7799039 or -2,548G > A	PCR-RFLP	MS	Phenotypic risk	The results did not show any significant association between clinical parameters (including the EDSS score, progression index and the age of disease onset) and different studies genotypes of LEP gene polymorphisms. Also, there were no significant differences in the distributions of LEP rs7799039 genotypes in MS patients with different types of the disease .	MS is mainly considered a Th1-mediated inflammatory disease,although recent studies postulate a vital role for helper T cells-17 (Th17 cells) in the pathogenesis of the disease .Therefore, the pathogenesis of MS is influenced by factors that affect the deviation of nave CD4+ Th cells towards Th1 or Th17 cells.Among different factors, the effects of adipokines such as adiponectin and leptin on Th cell deviation have recently drawn much attention.	30219158	Details
ADIPOQ	SNP	rs1501299 or +276G > T	PCR-RFLP	MS	Disease risk	rs1501299 (+276G>T) polymorphism in the second exon of ADIPOQ gene also showed a significant association with MS susceptibility in male patients.In fact, the frequency of rs1501299 intermediate+low adiponectin producer genotypes (TG+GG) and low adiponectin producer allele (rs1501299G) were significantly higher in male patients compared to male controls.	MS is mainly considered a Th1-mediated inflammatory disease,although recent studies postulate a vital role for helper T cells-17 (Th17 cells) in the pathogenesis of the disease .Therefore, the pathogenesis of MS is influenced by factors that affect the deviation of nave CD4+ Th cells towards Th1 or Th17 cells.Among different factors, the effects of adipokines such as adiponectin and leptin on Th cell deviation have recently drawn much attention.	30219158	Details
ADIPOQ	SNP	rs266729 or -11,377C > G	PCR-RFLP	MS	Disease risk	The frequency of low adiponectin producer rs266729GG genotype showed a sex-biased significant increase in male patients compared to male controls.The same comparison at the rs266729G allele showed significant increases in low adiponectin producer G allele in male patients compared to male controls .	MS is mainly considered a Th1-mediated inflammatory disease,although recent studies postulate a vital role for helper T cells-17 (Th17 cells) in the pathogenesis of the disease .Therefore, the pathogenesis of MS is influenced by factors that affect the deviation of nave CD4+ Th cells towards Th1 or Th17 cells.Among different factors, the effects of adipokines such as adiponectin and leptin on Th cell deviation have recently drawn much attention.	30219158	Details
ADIPOQ	SNP	rs1501299 or +276G > T	PCR-RFLP	MS	Phenotypic risk	Among studied SNPs, rs1501299 in ADIPOQ showed a significant association with susceptibility to development of PP-MS.In fact, comparison of adiponectin rs1501299TT genotype and rs1501299G allele carriers (GT+GG) showed that the frequency of rs1501299TT genotype is significantly higher in PP-MS compared to SP-MS+RR-MS patients.	MS is mainly considered a Th1-mediated inflammatory disease,although recent studies postulate a vital role for helper T cells-17 (Th17 cells) in the pathogenesis of the disease .Therefore, the pathogenesis of MS is influenced by factors that affect the deviation of nave CD4+ Th cells towards Th1 or Th17 cells.Among different factors, the effects of adipokines such as adiponectin and leptin on Th cell deviation have recently drawn much attention.	30219158	Details
CD45	mutation	C77G	PCR-RFLP	MS	Disease risk	All 272 subjects showed homozygosity inthe CD45 exon4, suggesting that this mutationis absent or very rare in Japanese population.	N/A	14641523	Details
IL6	polymorphisms	N/A	PCR-RFLP analysis	MS	Phenotypic risk	The -597/-174 IL-6pr genotypes have no major role in susceptibility to MS and in determining the clinical course of the disease or age of onset.	N/A	11574109	Details
ANKRD55	SNP	rs6859219	PCR-RFLP,TaqMan SNP	MS	Disease risk	We could successfully replicate the association of ANKRD55 (rs6859219) with susceptibility to MS in the Iranian population.	N/A	33491520	Details
MMEL1	SNP	rs3748816	PCR-RFLP,TaqMan SNP	MS	N/A	There was no significant difference in genotypic frequencies of SNP rs3748816 in MMEL1.	N/A	33491520	Details
CXCL12	polymorphism	SDF-13'a	PCR-RLFP	MS	Disease risk	Our results showed a significant difference between the A/A, A/G, and G/G genotype and A and G alleles of polymorphisms at position +801 of SDF-1α (CXCL12).	Immune regulatory factors might influence the pathogenesis of MS. Chemokines are low molecular weight proteins. A chemokine network exists in the CNS which is involved in physiological responses, under certain circumstances, pathological and repair processes subsequent to neurological injury.Based on the significant role that CXCL12 axis plays in hematopoiesis including hematopoietic cell differentiation and survival and homing of hematopoietic progenitors to the bone marrow and regulation of neuronal progenitor cell migration in the CNS, thus, genetic factors that lead to elevated expression of this chemokine enable the immune system to induce a vigorous immune response against CNS antigens in MS patients.	22125123	Details
NRG1	SNP	rs6994992	PCR-RLFP	MS	Disease risk	No significant difference in the allelic and genotype frequencies of the NRG1 polymorphism between MS patients and control group in Iranian population.	Neuregulin 1 (NRG1) is a signaling protein that mediates cell–cell interactions and plays critical roles in the growth of the nervous system. This gene has isoforms which are generated through alternative splicing and different promoter usage.	25802071	Details
NRG1	SNP	rs6994992	PCR-RLFP	MS	Phenotypic risk	By classification for clinical MS groups, significant difference in the genotype frequency was observed between SPMS patients and controls for SNP rs6994992 and also, a significant difference in the allelic distributions between PPMS patients and controls was revealed;there was a significant shift in frequency of C allele between PPMS group vs. other type of MS.	Neuregulin 1 (NRG1) is a signaling protein that mediates cell–cell interactions and plays critical roles in the growth of the nervous system. This gene has isoforms which are generated through alternative splicing and different promoter usage.	25802071	Details
HNMT	polymorphism	Thr/Ile	PCR-RLFP	MS	Disease risk	The frequencies of HNMT genotypes and HNMTIle alleles in patients with MS did not differ significantly from those of controls.	Histamine N-methyltransferase (HNMT) is the main metabolizing enzyme of histamine (a mediator of inflammation implicated in the pathogenesis of multiple sclerosis-MS) in the CNS.	19538200	Details
PON1	N/A	polymorphism、genotypes and allelic variants	PCR-RLFP	MS	Disease risk	The OR (95% confidence intervals) for the variant alleles PON155L and PON1-192R were 0.96 (0.73–1.26) and 1.01 (0.76–1.35), respectively	The high variability in the activity of PON1 has been attributed to several polymorphisms within the gene	19826962	Details
TNFSF10	polymorphism	N/A	PCR-SSCP	MS	Disease risk	Significant differences were found neither between MS patients and healthy controls nor between different disease courses.	Both elimination of T cells and damage to the CNS by immune cells are central pathogenic mechanisms of MS. While elimination of T cells by apoptosis is a physiological control mechanism, tissue damage in the CNS is a pathophysiological feature. During the past few years, several death receptor/ ligand systems mediating apoptosis have been discovered. We could previously show that TRAIL is able to induce massive neuronal cell destruction in the human brain.Since TRAIL receptors, but not the ligand, are expressed in the normal human brain and human antigen-specific T cells upregulate TRAIL upon activation, we expected a role of the TRAIL system in neuroinflammation.	15020080	Details
OMG	mutation	N/A	PCR-SSCP	MS	disease risk	This makes it unlikely that either of these genes is involved in genetic suscepti bility to MS, but regions of these genes outside of the exonic sequences have not been examined.	N/A	7477728	Details
EVI2A	mutation	N/A	PCR-SSCP	MS	disease risk	This makes it unlikely that either of these genes is involved in genetic suscepti bility to MS, but regions of these genes outside of the exonic sequences have not been examined.	N/A	7477728	Details
EVI2A	mutation	N/A	PCR-SSCP	MS	disease risk	This makes it unlikely that either of these genes is involved in genetic suscepti bility to MS, but regions of these genes outside of the exonic sequences have not been examined.	N/A	7477728	Details
EVI2A	polymorphism	N/A	PCR-SSCP	MS	disease risk	This makes it unlikely that either of these genes is involved in genetic suscepti bility to MS, but regions of these genes outside of the exonic sequences have not been examined.	N/A	7477728	Details
POLG	POLG CAG repeat length	N/A	PCR-SSCP	MS	Disease risk	In both patients and controls, there was a strong predominance of the allele 10Q.We did not find a statistically significant difference between the two studied groups.The frequency of the common POLG variant among the MS patients was 92.5%, which was similar to the control group.CAG repeat lengths ranging from 10–12 were detected, but not larger, expanded repeats were found in the control subjects and MS patients.	Multiple Sclerosis (MS) is a chronic and a common inflammatory disorder of the central nervous system (CNS) characterized with myelin loss, progressive neurological dysfunction, gliosis, and unstable degrees of axonal pathology.Recently,other research suggests that disorders of the mitochondrial were present in patients with MS. The only known mitochondrial DNA (mtDNA) polymerase is DNA polymerase γ (POLG).The integrity of mtDNA is maintained by POLG. The length variation of the poly-Q may modulate enzyme function.Deletion analysis of the CAG repeat regions has shown that it may not effect enzymatic properties, but reasonably up-regulates the expression.This CAG repeat explanation underlies various neurodegenerative disorders.	25767537	Details
TBX21	polymorphisms	1514T > C	PCR-SSCP	MS	Disease risk	Strong association between the wild -1514T allele and MS susceptibility was found with the allelic frequency of 99.6% in patients vs. 95.1% in controls, and the CC genotype frequency of the TBX21 polymorphism (-1514T > C) reported potential protective effect against the disease.	The pathogenesis of MS is mediated by the development of auto-aggressive T-lymphocytes in peripheral immune organs, which migrate through the blood-brain barrier (BBB);thus, triggering inflammation, and eventually leading to demyelination and degeneration of axons.The developmental regulation of auto-reactive T-helper cells is mainly determined by various transcription factors such as T-bet, which involves with up-regulating the production of interferon gamma (IFNγ) in Th1 cell subtypes.Considering the autonomous activity of Th1 cells as one reason for MS, many evaluations have been done on T-bet transcription factor.T-bet is still necessary for the survival of Th17 cells through regulating the expression of the IL-23 receptor.	30886677	Details
HRES1	allelic	N/A	PCR-SSCP	MS	Disease risk	However, we found a significant difference in the distribution of these alleles between a group of 87 MS patients and a control group of 158 healthy individuals (P = 0.014). There were no differences in the distribution of the HRES-1 allelic forms between MS patients with a relapsing-remitting course and patients with chronic progressive MS.	N/A	9345377	Details
HLA-DRB1	allele	N/A	PCR-SSCP and PCRRFLP	MS	Disease risk	We found HLA DR 13 was more frequent in healthy controls than in RRMS patients, suggesting a protective factor among Mexican Mestizo population.	MHC II type-specific antigens are able to display specific viral epitopes that stimulate a T cell response with the following efficient elimination of the virus. It is possible that in MS patients with the DR 13 allele the efficiency in antigen presentation is able to influence disease progression.	26367070	Details
HLA-A	Allele	NA	PCR-SSO	MS	Disease risk	No significant deviations in antigen frequencies between MS patients and control groups were observed.	The occurrence of CNMS in these epidemics seems therefore associated to HLA class II-linked genetic factors similar to those found in studies of other Caucasians with MS. This observation seems important in understanding the pathogenesis of this disease	7903488	Details
HLA-B	Allele	NA	PCR-SSO	MS	Disease risk	No significant deviations in antigen frequencies between MS patients and control groups were observed.	The occurrence of CNMS in these epidemics seems therefore associated to HLA class II-linked genetic factors similar to those found in studies of other Caucasians with MS. This observation seems important in understanding the pathogenesis of this disease	7903488	Details
HLA-DRB1	Allele	NA	PCR-SSO	MS	Disease risk	whereas the class I1 antigens do deviate: 50% of the Faroese MS patients carry the HLA-DR2 (DQI lDRB 15) antigen, compared to a frequency of 15-2ou/0 among the control groups.	The occurrence of CNMS in these epidemics seems therefore associated to HLA class II-linked genetic factors similar to those found in studies of other Caucasians with MS. This observation seems important in understanding the pathogenesis of this disease	7903488	Details
HLA-DRB1	allele	DRB1*1501	PCR-SSO and PCR-SSP	MS	Phenotypic risk	DRB1*1501 is associated with the presence of MS only in females and with lower severity of the disease only in males.	N/A	14752708	Details
HLA-DRB1	DRB5 * 0101	N/A	PCR-SSOP	MS	Disease risk	In this relatively homogeneous ethnic group, MS was positively associated with DRB5*0101, DQB1*0602, and DQA1*0102 and negatively associated with DQB1*0301.	N/A	1429036	Details
HLA-DQB1	DQB1*0602	N/A	PCR-SSOP	MS	Disease risk	In this relatively homogeneous ethnic group, MS was positively associated with DRB5*0101, DQB1*0602, and DQA1*0102 and negatively associated with DQB1*0301.	N/A	1429036	Details
HLA-DQA1	DQA1*0102	N/A	PCR-SSOP	MS	Disease risk	In this relatively homogeneous ethnic group, MS was positively associated with DRB5*0101, DQB1*0602, and DQA1*0102 and negatively associated with DQB1*0301.	N/A	1429036	Details
HLA-A	allele	N/A	PCR-SSOP	MS	Disease risk ; Phenotypic risk	No statistically significant difference in the frequencies of HLA-A alleles was found between controls and total MS patients, Western type MS patients, Asian type MS patients or between the two subtypes.	N/A	9894852	Details
HLA-B	allele	N/A	PCR-SSOP	MS	Disease risk ; Phenotypic risk	After Bonferroni corrections were made there was no statistical significance in the association between HLA-B*5101 alleles and MS in total MS patients and controls.In addition there was no statistical significant difference in frequencies of HLA-B alleles between the two subgroups.	N/A	9894852	Details
HLA-DRB1	allele	N/A	PCR-SSOP	MS	Disease risk	Positive association between total MS patients and controls was observed in HLA-DRB1*1501.The frequency of DRB1*0901 was decreased in total MS as well as in both Western and Asian type MS. The frequency of HLA DRB1*1501 was increased in Western type MS compared with controls.The frequency of DRB1*1501 did not differ significantly between patients with Asian type MS and controls. The frequency of DRB1*0802 was however increased in Asian type MS when compared with controls.	N/A	9894852	Details
HLA-DRB1	allele	N/A	PCR-SSOP	MS	Phenotypic risk	After Bonferroni correction there was no statistically significant difference in the allele frequency of the between two subtypes.	N/A	9894852	Details
HLA-DRB1	SNP	HLA-DRB1*1501, DRB1*04, DQB1*02,DQB1*0302, DQB1*0602	PCR-SSOP	MS	Disease risk	Evidence for excess transmission to affected individuals was observed for HLA-DRB1*1501, DRB1*04, DQB1*02, and DQB1*0302 alleles, but not for DQB1*0602 using PDT or TRANSMIT.When HLA alleles were analyzed as haplotypes, we observed an excess transmission for the DRB1*0400, DQB1*0302 haplotype. The DR2 haplotype (DRB1*1501, DQB1*0602) was borderline significant. DRB1*1501, X and DRB1*04, X haplotypes were also examined, where X was not DQB1*0602 or *0302.Both haplotypes displayed suggestive evidence for over-transmission, providing additional support for a primary DRB1 effect. However, these results were not significant. The DR3 haplotype was negative. As observed in other populations,HLA-DR3 confers low relative risk.The effect of HLA on age at onset, initial symptom, disease course, and endpoints of clinical severity was evaluated in patients stratified by the presence or absence of DRB1*1501 or DRB1*04. No significant effect of DRB1 was present.	N/A	15668443	Details
CCR5	genotype	DRB1*15 + TGFB1*T + CCR5*d	PCR-SSP	MS	Disease risk	Carriers of the most significant combinations: DRB1*15 + TGFB1*T + CCR5*d + IFNAR1*G and DRB1*15 + TGFB1*T + CCR5*d (permutation p-values: 0.0056 and 0.013, respectively) had a 14 to 15-times increased risk of ineffective response to GA therapy.	N/A	22111603	Details
HLA-DRB1	genotype	DRB1*15 + TGFB1*T + CCR5*d + IFNAR1*G	PCR-SSP	MS	Disease risk	Carriers of the most significant combinations: DRB1*15 + TGFB1*T + CCR5*d + IFNAR1*G and DRB1*15 + TGFB1*T + CCR5*d (permutation p-values: 0.0056 and 0.013, respectively) had a 14 to 15-times increased risk of ineffective response to GA therapy.	N/A	22111603	Details
TGFB1	genotype	DRB1*15 + TGFB1*T + CCR5*d + IFNAR1*G	PCR-SSP	MS	Disease risk	Carriers of the most significant combinations: DRB1*15 + TGFB1*T + CCR5*d + IFNAR1*G and DRB1*15 + TGFB1*T + CCR5*d (permutation p-values: 0.0056 and 0.013, respectively) had a 14 to 15-times increased risk of ineffective response to GA therapy.	N/A	22111603	Details
CCR5	genotype	DRB1*15 + TGFB1*T + CCR5*d + IFNAR1*G	PCR-SSP	MS	Disease risk	Carriers of the most significant combinations: DRB1*15 + TGFB1*T + CCR5*d + IFNAR1*G and DRB1*15 + TGFB1*T + CCR5*d (permutation p-values: 0.0056 and 0.013, respectively) had a 14 to 15-times increased risk of ineffective response to GA therapy.	N/A	22111603	Details
IFNAR1	genotype	DRB1*15 + TGFB1*T + CCR5*d + IFNAR1*G	PCR-SSP	MS	Disease risk	Carriers of the most significant combinations: DRB1*15 + TGFB1*T + CCR5*d + IFNAR1*G and DRB1*15 + TGFB1*T + CCR5*d (permutation p-values: 0.0056 and 0.013, respectively) had a 14 to 15-times increased risk of ineffective response to GA therapy.	N/A	22111603	Details
HLA-DRB1	polymorphisms	DRB1*01	PCR-SSP	MS	Disease risk	Phenotype frequency of HLA-DRB1 alleles in MS patients and healthy controls	N/A	17412364	Details
HLA-DRB1	polymorphisms	DRB1*03	PCR-SSP	MS	Disease risk	The HLA-DRB103 allele was positively associated with MS in the overall patient population.	N/A	17412364	Details
HLA-DRB1	polymorphisms	DRB1*04	PCR-SSP	MS	Disease risk	Phenotype frequency of HLA-DRB1 alleles in MS patients and healthy controls	N/A	17412364	Details
HLA-DRB1	polymorphisms	DRB1*07	PCR-SSP	MS	Disease risk	Phenotype frequency of HLA-DRB1 alleles in MS patients and healthy controls	N/A	17412364	Details
HLA-DRB1	polymorphisms	DRB1*08	PCR-SSP	MS	Disease risk	Phenotype frequency of HLA-DRB1 alleles in MS patients and healthy controls	N/A	17412364	Details
HLA-DRB1	polymorphisms	DRB1*09	PCR-SSP	MS	Disease risk	Phenotype frequency of HLA-DRB1 alleles in MS patients and healthy controls	N/A	17412364	Details
HLA-DRB1	polymorphisms	DRB1*10	PCR-SSP	MS	Disease risk	Phenotype frequency of HLA-DRB1 alleles in MS patients and healthy controls	N/A	17412364	Details
HLA-DRB1	polymorphisms	DRB1*11	PCR-SSP	MS	Disease risk	Phenotype frequency of HLA-DRB1 alleles in MS patients and healthy controls	N/A	17412364	Details
HLA-DRB1	polymorphisms	DRB1*12	PCR-SSP	MS	Disease risk	Phenotype frequency of HLA-DRB1 alleles in MS patients and healthy controls	N/A	17412364	Details
HLA-DRB1	polymorphisms	DRB1*13	PCR-SSP	MS	Disease risk	Phenotype frequency of HLA-DRB1 alleles in MS patients and healthy controls	N/A	17412364	Details
HLA-DRB1	polymorphisms	DRB1*14	PCR-SSP	MS	Disease risk	Phenotype frequency of HLA-DRB1 alleles in MS patients and healthy controls	N/A	17412364	Details
HLA-DRB1	polymorphisms	DRB1*15	PCR-SSP	MS	Disease risk	HLA-DRB115 occurred more frequently in the group with benign disease and in the group with non-benign disease compared with controls.	N/A	17412364	Details
HLA-DRB1	polymorphisms	DRB1*16	PCR-SSP	MS	Disease risk	Phenotype frequency of HLA-DRB1 alleles in MS patients and healthy controls	N/A	17412364	Details
FasL	allel	A	PCR-SSP	MS	Disease risk	The HLA DRB1 1501–DQB1 0602 haplotype is associated with B allele with a relative frequency higher than A allele 0.52 and 0.48 in patients vs. 0.68 and 0.32 in controls .	N/A	11438180	Details
FasL	allel	B	PCR-SSP	MS	Disease risk	The HLA DRB1 1501–DQB1 0602 haplotype is associated with B allele with a relative frequency higher than A allele 0.52 and 0.48 in patients vs. 0.68 and 0.32 in controls .	N/A	11438180	Details
TNF	gene polymorphisms	A (/ 238 allele	PCR-SSP	MS	Disease risk	Remarkable results were obtained for IL-2 GG (/ 330 genotype (P0/ 0.06), IL-6 C (/ 174 allele (P0/ 0.06), CG and GG genotypes (PB/ 0.001), and GG (P0/ 0.02) and CG (PB/ 0.001) haplotypes, and TNF-a A (/ 238 allele (PB/ 0.001), GG (P0/ 0.003) and GA (PB/ 0.001) haplotypes. These results suggest that polymorphic variations of these pro-inflammatory cytokines play an important role in susceptibility to MS.	gene polymorphisms	17439892	Details
TNF	gene polymorphisms	GGhaplotypes	PCR-SSP	MS	Disease risk	Remarkable results were obtained for IL-2 GG (/ 330 genotype (P0/ 0.06), IL-6 C (/ 174 allele (P0/ 0.06), CG and GG genotypes (PB/ 0.001), and GG (P0/ 0.02) and CG (PB/ 0.001) haplotypes, and TNF-a A (/ 238 allele (PB/ 0.001), GG (P0/ 0.003) and GA (PB/ 0.001) haplotypes. These results suggest that polymorphic variations of these pro-inflammatory cytokines play an important role in susceptibility to MS.	gene polymorphisms	17439892	Details
TNF	gene polymorphisms	GAhaplotypes	PCR-SSP	MS	Disease risk	Remarkable results were obtained for IL-2 GG (/ 330 genotype (P0/ 0.06), IL-6 C (/ 174 allele (P0/ 0.06), CG and GG genotypes (PB/ 0.001), and GG (P0/ 0.02) and CG (PB/ 0.001) haplotypes, and TNF-a A (/ 238 allele (PB/ 0.001), GG (P0/ 0.003) and GA (PB/ 0.001) haplotypes. These results suggest that polymorphic variations of these pro-inflammatory cytokines play an important role in susceptibility to MS.	gene polymorphisms	17439892	Details
IL2	gene polymorphisms	GG (/ 330 genotype	PCR-SSP	MS	Disease risk	Remarkable results were obtained for IL-2 GG (/ 330 genotype (P0/ 0.06), IL-6 C (/ 174 allele (P0/ 0.06), CG and GG genotypes (PB/ 0.001), and GG (P0/ 0.02) and CG (PB/ 0.001) haplotypes, and TNF-a A (/ 238 allele (PB/ 0.001), GG (P0/ 0.003) and GA (PB/ 0.002) haplotypes. These results suggest that polymorphic variations of these pro-inflammatory cytokines play an important role in susceptibility to MS.	gene polymorphisms	17439892	Details
IL6	gene polymorphisms	C (/ 174 allele	PCR-SSP	MS	Disease risk	Remarkable results were obtained for IL-2 GG (/ 330 genotype (P0/ 0.06), IL-6 C (/ 174 allele (P0/ 0.06), CG and GG genotypes (PB/ 0.001), and GG (P0/ 0.02) and CG (PB/ 0.001) haplotypes, and TNF-a A (/ 238 allele (PB/ 0.001), GG (P0/ 0.003) and GA (PB/ 0.003) haplotypes. These results suggest that polymorphic variations of these pro-inflammatory cytokines play an important role in susceptibility to MS.	gene polymorphisms	17439892	Details
IL6	gene polymorphisms	CGhaplotypes	PCR-SSP	MS	Disease risk	Remarkable results were obtained for IL-2 GG (/ 330 genotype (P0/ 0.06), IL-6 C (/ 174 allele (P0/ 0.06), CG and GG genotypes (PB/ 0.001), and GG (P0/ 0.02) and CG (PB/ 0.001) haplotypes, and TNF-a A (/ 238 allele (PB/ 0.001), GG (P0/ 0.003) and GA (PB/ 0.003) haplotypes. These results suggest that polymorphic variations of these pro-inflammatory cytokines play an important role in susceptibility to MS.	gene polymorphisms	17439892	Details
IL6	gene polymorphisms	GGhaplotypes	PCR-SSP	MS	Disease risk	Remarkable results were obtained for IL-2 GG (/ 330 genotype (P0/ 0.06), IL-6 C (/ 174 allele (P0/ 0.06), CG and GG genotypes (PB/ 0.001), and GG (P0/ 0.02) and CG (PB/ 0.001) haplotypes, and TNF-a A (/ 238 allele (PB/ 0.001), GG (P0/ 0.003) and GA (PB/ 0.003) haplotypes. These results suggest that polymorphic variations of these pro-inflammatory cytokines play an important role in susceptibility to MS.	gene polymorphisms	17439892	Details
IL6	gene polymorphisms	GGgenotypes	PCR-SSP	MS	Disease risk	Remarkable results were obtained for IL-2 GG (/ 330 genotype (P0/ 0.06), IL-6 C (/ 174 allele (P0/ 0.06), CG and GG genotypes (PB/ 0.001), and GG (P0/ 0.02) and CG (PB/ 0.001) haplotypes, and TNF-a A (/ 238 allele (PB/ 0.001), GG (P0/ 0.003) and GA (PB/ 0.003) haplotypes. These results suggest that polymorphic variations of these pro-inflammatory cytokines play an important role in susceptibility to MS.	gene polymorphisms	17439892	Details
IL6	gene polymorphisms	CGgenotypes	PCR-SSP	MS	Disease risk	Remarkable results were obtained for IL-2 GG (/ 330 genotype (P0/ 0.06), IL-6 C (/ 174 allele (P0/ 0.06), CG and GG genotypes (PB/ 0.001), and GG (P0/ 0.02) and CG (PB/ 0.001) haplotypes, and TNF-a A (/ 238 allele (PB/ 0.001), GG (P0/ 0.003) and GA (PB/ 0.003) haplotypes. These results suggest that polymorphic variations of these pro-inflammatory cytokines play an important role in susceptibility to MS.	gene polymorphisms	17439892	Details
HLA-DRB1	polymorphisms	DRB1*01	PCR-SSP	MS	Disease risk	HLA-DRB1 allele frequencies in the Mulatto sample of patients showing relapsing/remitting multiple sclerosis (MS) and healthy Mulatto controls	N/A	17681614	Details
HLA-DRB1	polymorphisms	DRB1*03	PCR-SSP	MS	Disease risk	HLA-DRB1 allele frequencies in the Mulatto sample of patients showing relapsing/remitting multiple sclerosis (MS) and healthy Mulatto controls	N/A	17681614	Details
HLA-DRB1	polymorphisms	DRB1*04	PCR-SSP	MS	Disease risk	HLA-DRB1 allele frequencies in the Mulatto sample of patients showing relapsing/remitting multiple sclerosis (MS) and healthy Mulatto controls	N/A	17681614	Details
HLA-DRB1	polymorphisms	DRB1*07	PCR-SSP	MS	Disease risk	HLA-DRB1 allele frequencies in the Mulatto sample of patients showing relapsing/remitting multiple sclerosis (MS) and healthy Mulatto controls	N/A	17681614	Details
HLA-DRB1	polymorphisms	DRB1*08	PCR-SSP	MS	Disease risk	HLA-DRB1 allele frequencies in the Mulatto sample of patients showing relapsing/remitting multiple sclerosis (MS) and healthy Mulatto controls	N/A	17681614	Details
HLA-DRB1	polymorphisms	DRB1*09	PCR-SSP	MS	Disease risk	HLA-DRB1 allele frequencies in the Mulatto sample of patients showing relapsing/remitting multiple sclerosis (MS) and healthy Mulatto controls	N/A	17681614	Details
HLA-DRB1	polymorphisms	DRB1*010	PCR-SSP	MS	Disease risk	HLA-DRB1 allele frequencies in the Mulatto sample of patients showing relapsing/remitting multiple sclerosis (MS) and healthy Mulatto controls	N/A	17681614	Details
HLA-DRB1	polymorphisms	DRB1*11	PCR-SSP	MS	Disease risk	HLA-DRB1 allele frequencies in the Mulatto sample of patients showing relapsing/remitting multiple sclerosis (MS) and healthy Mulatto controls	N/A	17681614	Details
HLA-DRB1	polymorphisms	DRB1*13	PCR-SSP	MS	Disease risk	HLA-DRB1 allele frequencies in the Mulatto sample of patients showing relapsing/remitting multiple sclerosis (MS) and healthy Mulatto controls	N/A	17681614	Details
HLA-DRB1	polymorphisms	DRB1*14	PCR-SSP	MS	Disease risk	HLA-DRB1 allele frequencies in the Mulatto sample of patients showing relapsing/remitting multiple sclerosis (MS) and healthy Mulatto controls	N/A	17681614	Details
HLA-DRB1	polymorphisms	DRB1*12	PCR-SSP	MS	Disease risk	HLA-DRB1 allele frequencies in the Mulatto sample of patients showing relapsing/remitting multiple sclerosis (MS) and healthy Mulatto controls	N/A	17681614	Details
HLA-DRB1	polymorphisms	DRB1*16	PCR-SSP	MS	Disease risk	HLA-DRB1 allele frequencies in the Mulatto sample of patients showing relapsing/remitting multiple sclerosis (MS) and healthy Mulatto controls	N/A	17681614	Details
HLA-DRB1	polymorphisms	DRB1*1502	PCR-SSP	MS	Disease risk	In contrast with the observations concerning the White sample, the DRB11503 allele (p= 0.0244; OR = 4.61), instead of DRB11501 (p= 0.2389; OR = 2.39), was also associated with MS susceptibility.	N/A	17681614	Details
HLA-DRB1	polymorphisms	DRB1*1501	PCR-SSP	MS	Disease risk	HLA-DRB1 allele frequencies in the Mulatto sample of patients showing relapsing/remitting multiple sclerosis (MS) and healthy Mulatto controls	N/A	17681614	Details
HLA-DRB1	polymorphisms	DRB1*1503	PCR-SSP	MS	Disease risk	In contrast with the observations concerning the White sample, the DRB11503 allele (p= 0.0244; OR = 4.61), instead of DRB11501 (p= 0.2389; OR = 2.39), was also associated with MS susceptibility.	N/A	17681614	Details
HLA-DRB1	polymorphisms	DRB1*15	PCR-SSP	MS	Disease risk	Disease susceptibility was confirmed for the DRB115 allele group (p = 0.0024; OR = 4.28).	N/A	17681614	Details
HLA-DQB1	allele	HLA-DQB1*0602	PCR-SSP	MS	Disease risk	Results revealed that distribution of mentioned allele was not statistically different among cases and controls;furthermore, no association was shown between this allele and gender, ethnicity or type of disease.	N/A	26443252	Details
HLA-DRB1	allele	residue 86 polymorphism	PCR-SSP	MS	Disease risk	There was a highly significant increase in the Val/Val genotype in the MS patients and a significant decrease in the Gly/Gly genotype.The Val/Gly genotype was decreased in the MS patients, though not significantly.There was also a highly significant decrease in the Gly phenotype in the MS patients and a significant increase in the Val phenotype.	N/A	10439317	Details
HLA-DRB1	allele	N/A	PCR-SSP	MS	Disease risk	An association of MS with HLA-DRB1*15 was found (14.7% vs 3.8%, OR (95% CI)=4.34 (1.69-11.39), p(c)=2.5×10(-3)) after Bonferroni's correction. Moreover, the DRB1*15-DQB1*06 (13.8% vs 2.8%, OR (95% CI)=5.44 (1.92-17.41), p(c)=1.1×10(-3)) and DRB1*04-DQB1*04 (8.6% vs 1.9%, OR (95% CI)=4.86 (1.36-21.62), p(c)=0.028) haplotypes were found to confer a susceptibility to multiple sclerosis.	N/A	20691532	Details
HLA-DRB1	genotype	DR1	PCR-SSP	MS	Phenotype risk	These results suggest that the MS susceptibility gene, HLA-DR(2)15 type, does not induce MSIT, and conceivably these are two separate risk factors in the development of MS.	Hence, the HLA locus may be involved in the initialpathogenic events, while other candidate QTL, such as those postulated for MSIT, influence the development and progression of the disease.	17463066	Details
HLA-DRB1	genotype	DR(2)15	PCR-SSP	MS	Phenotype risk	These results suggest that the MS susceptibility gene, HLA-DR(2)15 type, does not induce MSIT, and conceivably these are two separate risk factors in the development of MS.	Hence, the HLA locus may be involved in the initialpathogenic events, while other candidate QTL, such as those postulated for MSIT, influence the development and progression of the disease.	17463066	Details
HLA-DRB1	genotype	DR3	PCR-SSP	MS	Phenotype risk	These results suggest that the MS susceptibility gene, HLA-DR(2)15 type, does not induce MSIT, and conceivably these are two separate risk factors in the development of MS.	Hence, the HLA locus may be involved in the initialpathogenic events, while other candidate QTL, such as those postulated for MSIT, influence the development and progression of the disease.	17463066	Details
HLA-DRB1	genotype	DR4	PCR-SSP	MS	Phenotype risk	These results suggest that the MS susceptibility gene, HLA-DR(2)15 type, does not induce MSIT, and conceivably these are two separate risk factors in the development of MS.	Hence, the HLA locus may be involved in the initialpathogenic events, while other candidate QTL, such as those postulated for MSIT, influence the development and progression of the disease.	17463066	Details
HLA-DRB1	genotype	DR5	PCR-SSP	MS	Phenotype risk	These results suggest that the MS susceptibility gene, HLA-DR(2)15 type, does not induce MSIT, and conceivably these are two separate risk factors in the development of MS.	Hence, the HLA locus may be involved in the initialpathogenic events, while other candidate QTL, such as those postulated for MSIT, influence the development and progression of the disease.	17463066	Details
HLA-DRB1	genotype	DR6	PCR-SSP	MS	Phenotype risk	These results suggest that the MS susceptibility gene, HLA-DR(2)15 type, does not induce MSIT, and conceivably these are two separate risk factors in the development of MS.	Hence, the HLA locus may be involved in the initialpathogenic events, while other candidate QTL, such as those postulated for MSIT, influence the development and progression of the disease.	17463066	Details
HLA-DRB1	genotype	DR7	PCR-SSP	MS	Phenotype risk	These results suggest that the MS susceptibility gene, HLA-DR(2)15 type, does not induce MSIT, and conceivably these are two separate risk factors in the development of MS.	Hence, the HLA locus may be involved in the initialpathogenic events, while other candidate QTL, such as those postulated for MSIT, influence the development and progression of the disease.	17463066	Details
HLA-DRB1	genotype	DR8	PCR-SSP	MS	Phenotype risk	These results suggest that the MS susceptibility gene, HLA-DR(2)15 type, does not induce MSIT, and conceivably these are two separate risk factors in the development of MS.	Hence, the HLA locus may be involved in the initialpathogenic events, while other candidate QTL, such as those postulated for MSIT, influence the development and progression of the disease.	17463066	Details
HLA-DRB1	genotype	DR9	PCR-SSP	MS	Phenotype risk	These results suggest that the MS susceptibility gene, HLA-DR(2)15 type, does not induce MSIT, and conceivably these are two separate risk factors in the development of MS.	Hence, the HLA locus may be involved in the initialpathogenic events, while other candidate QTL, such as those postulated for MSIT, influence the development and progression of the disease.	17463066	Details
HLA-DRB1	genotype	DR10	PCR-SSP	MS	Phenotype risk	These results suggest that the MS susceptibility gene, HLA-DR(2)15 type, does not induce MSIT, and conceivably these are two separate risk factors in the development of MS.	Hence, the HLA locus may be involved in the initialpathogenic events, while other candidate QTL, such as those postulated for MSIT, influence the development and progression of the disease.	17463066	Details
HLA-DRB1	genotype	DR11	PCR-SSP	MS	Phenotype risk	These results suggest that the MS susceptibility gene, HLA-DR(2)15 type, does not induce MSIT, and conceivably these are two separate risk factors in the development of MS.	Hence, the HLA locus may be involved in the initialpathogenic events, while other candidate QTL, such as those postulated for MSIT, influence the development and progression of the disease.	17463066	Details
HLA-DRB1	genotype	DR12	PCR-SSP	MS	Phenotype risk	These results suggest that the MS susceptibility gene, HLA-DR(2)15 type, does not induce MSIT, and conceivably these are two separate risk factors in the development of MS.	Hence, the HLA locus may be involved in the initialpathogenic events, while other candidate QTL, such as those postulated for MSIT, influence the development and progression of the disease.	17463066	Details
HLA-DRB1	genotype	DR13	PCR-SSP	MS	Phenotype risk	These results suggest that the MS susceptibility gene, HLA-DR(2)15 type, does not induce MSIT, and conceivably these are two separate risk factors in the development of MS.	Hence, the HLA locus may be involved in the initialpathogenic events, while other candidate QTL, such as those postulated for MSIT, influence the development and progression of the disease.	17463066	Details
HLA-DRB1	genotype	DR14	PCR-SSP	MS	Phenotype risk	These results suggest that the MS susceptibility gene, HLA-DR(2)15 type, does not induce MSIT, and conceivably these are two separate risk factors in the development of MS.	Hence, the HLA locus may be involved in the initialpathogenic events, while other candidate QTL, such as those postulated for MSIT, influence the development and progression of the disease.	17463066	Details
TNF	Gene polymorphisms	exon 10 nt 1668*T-->G	PCR-SSP	MS	Disease risk	We found a significant association between exon 10 nt 1668*T-->G polymorphism and susceptibility to MS	Thus, TNFR II polymorphism appears to contuibute to the suscepbility to MS but not to its phenotype or clinical severity	14651520	Details
HLA-DRB1	genotype	DR103	PCR-SSP	MS	Phenotype risk	These results suggest that the MS susceptibility gene, HLA-DR(2)15 type, does not induce MSIT, and conceivably these are two separate risk factors in the development of MS.	Hence, the HLA locus may be involved in the initialpathogenic events, while other candidate QTL, such as those postulated for MSIT, influence the development and progression of the disease.	17463066	Details
TNF	Gene polymorphisms	exon 6 nt 676*T-->G	PCR-SSP	MS	Disease risk	The other investigated nucleotide substitutions were not associated with susceptibility to or clinical parameters in MS	Thus, TNFR II polymorphism appears to contuibute to the suscepbility to MS but not to its phenotype or clinical severity	14651520	Details
TNF	Gene polymorphisms	exon 6 nt 783*G-->A	PCR-SSP	MS	Disease risk	The other investigated nucleotide substitutions were not associated with susceptibility to or clinical parameters in MS	Thus, TNFR II polymorphism appears to contuibute to the suscepbility to MS but not to its phenotype or clinical severity	14651520	Details
TNF	Gene polymorphisms	exon 10 nt 1663*G-->A	PCR-SSP	MS	Disease risk	The other investigated nucleotide substitutions were not associated with susceptibility to or clinical parameters in MS	Thus, TNFR II polymorphism appears to contuibute to the suscepbility to MS but not to its phenotype or clinical severity	14651520	Details
TNF	Gene polymorphisms	exon 10 nt 1690*T-->C	PCR-SSP	MS	Disease risk	The other investigated nucleotide substitutions were not associated with susceptibility to or clinical parameters in MS	Thus, TNFR II polymorphism appears to contuibute to the suscepbility to MS but not to its phenotype or clinical severity	14651520	Details
IFNG	polymorphisms	at position +874	PCR-SSP	MS	Disease risk	There is no association between IFN- gamma +874 polymorphism and MS susceptibility or severity of the disease.	N/A	17301401	Details
CCL7	Allele	NA	PCR-SSP	MS	Disease risk	We conclude that the MCP-3)A4 allele might protect against MS development on the background of the increased risk in HLA-DRB1)15q individuals and the MCP-3)A2 allele seems protective in low-risk individuals, who are both negative for DRB1)03 and DRB1)15.	Monocyte chemotactic protein 3 MCP-3 is a chemokine that attracts mononuclear cells, including monocytes and lymphocytes, the inflammatory cell types that predominate in multiple sclerosis lesions.	10229131	Details
HLA-DQB1	DQB1*0303	N/A	PCR-SSP	MS	Disease risk	We also found that the DQB1*0303 allele was significantly associated with disease severity (mean Multiple Sclerosis Severity Score difference = 1.979, P = 0.002).	N/A	22404765	Details
HAVCR1	SNP	rs7702920	PCR-SSP	MS	Disease risk	Haplotype analysis of our data resulted in 11 haplotypes and showed no significant differences between MS patients and controls	Our findings suggest that even fine mapping of TIM1 shows no significant association of this gene with multiple sclerosis	20070602	Details
HAVCR1	SNP	rs41297577	PCR-SSP	MS	Disease risk	Haplotype analysis of our data resulted in 11 haplotypes and showed no significant differences between MS patients and controls	Our findings suggest that even fine mapping of TIM1 shows no significant association of this gene with multiple sclerosis	20070602	Details
HAVCR1	SNP	rs41297579	PCR-SSP	MS	Disease risk	Haplotype analysis of our data resulted in 11 haplotypes and showed no significant differences between MS patients and controls	Our findings suggest that even fine mapping of TIM1 shows no significant association of this gene with multiple sclerosis	20070602	Details
HAVCR1	SNP	rs9313422	PCR-SSP	MS	Disease risk	Haplotype analysis of our data resulted in 11 haplotypes and showed no significant differences between MS patients and controls	Our findings suggest that even fine mapping of TIM1 shows no significant association of this gene with multiple sclerosis	20070602	Details
HAVCR1	SNP	rs34333511	PCR-SSP	MS	Disease risk	Haplotype analysis of our data resulted in 11 haplotypes and showed no significant differences between MS patients and controls	Our findings suggest that even fine mapping of TIM1 shows no significant association of this gene with multiple sclerosis	20070602	Details
HAVCR1	SNP	rs1553316	PCR-SSP	MS	Disease risk	Haplotype analysis of our data resulted in 11 haplotypes and showed no significant differences between MS patients and controls	Our findings suggest that even fine mapping of TIM1 shows no significant association of this gene with multiple sclerosis	20070602	Details
HAVCR1	SNP	rs12522248	PCR-SSP	MS	Disease risk	Haplotype analysis of our data resulted in 11 haplotypes and showed no significant differences between MS patients and controls	Our findings suggest that even fine mapping of TIM1 shows no significant association of this gene with multiple sclerosis	20070602	Details
HAVCR1	SNP	rs1553318	PCR-SSP	MS	Disease risk	Haplotype analysis of our data resulted in 11 haplotypes and showed no significant differences between MS patients and controls	Our findings suggest that even fine mapping of TIM1 shows no significant association of this gene with multiple sclerosis	20070602	Details
HAVCR1	SNP	rs2279804	PCR-SSP	MS	Disease risk	Haplotype analysis of our data resulted in 11 haplotypes and showed no significant differences between MS patients and controls	Our findings suggest that even fine mapping of TIM1 shows no significant association of this gene with multiple sclerosis	20070602	Details
HAVCR1	SNP	rs2277025	PCR-SSP	MS	Disease risk	Haplotype analysis of our data resulted in 11 haplotypes and showed no significant differences between MS patients and controls	Our findings suggest that even fine mapping of TIM1 shows no significant association of this gene with multiple sclerosis	20070602	Details
HLA-DRB1	genotype	DRB1*15 + TGFB1*T + CCR5*d	PCR-SSP	MS	Disease risk	Carriers of the most significant combinations: DRB1*15 + TGFB1*T + CCR5*d + IFNAR1*G and DRB1*15 + TGFB1*T + CCR5*d (permutation p-values: 0.0056 and 0.013, respectively) had a 14 to 15-times increased risk of ineffective response to GA therapy.	N/A	22111603	Details
TGFB1	genotype	DRB1*15 + TGFB1*T + CCR5*d	PCR-SSP	MS	Disease risk	Carriers of the most significant combinations: DRB1*15 + TGFB1*T + CCR5*d + IFNAR1*G and DRB1*15 + TGFB1*T + CCR5*d (permutation p-values: 0.0056 and 0.013, respectively) had a 14 to 15-times increased risk of ineffective response to GA therapy.	N/A	22111603	Details
ATG5	polymorphisms	DRB1*01	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DRB1	polymorphisms	DRB1*03	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DRB1	polymorphisms	DRB1*04	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DRB1	polymorphisms	DRB1*07	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DRB1	polymorphisms	DRB1*08	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DRB1	polymorphisms	DRB1*09	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DRB1	polymorphisms	DRB1*010	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DRB1	polymorphisms	DRB1*11	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DRB1	polymorphisms	DRB1*12	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DRB1	polymorphisms	DRB1*13	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DRB1	polymorphisms	DRB1*14	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DRB1	polymorphisms	DRB1*15	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	A significant increase of DRB1*15 allele frequency and HLA-DRB1*15-DQB1*06 haplotype were observed in Moroccan MS patients.	N/A	23849771	Details
HLA-DRB1	polymorphisms	DRB1*16	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DQB1	polymorphisms	DQB1*02	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DQB1	polymorphisms	DQB1*03	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DQB1	polymorphisms	DQB1*04	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DQB1	polymorphisms	DQB1*05	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DQB1	polymorphisms	DQB1*06	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DRB1	polymorphisms	DR-DQ*04-03	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DRB1	polymorphisms	DR-DQ*03-02	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DRB1	polymorphisms	DR-DQ*07-02	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DRB1	polymorphisms	DR-DQ*03-06	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DRB1	polymorphisms	DR-DQ*15-06	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	A significant increase of DRB1*15 allele frequency and HLA-DRB1*15-DQB1*06 haplotype were observed in Moroccan MS patients.	N/A	23849771	Details
HLA-DRB1	polymorphisms	DR-DQ*01-05	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DRB1	polymorphisms	DR-DQ*03-03	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DRB1	polymorphisms	DR-DQ*11-03	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DQB1	polymorphisms	DR-DQ*04-03	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DQB1	polymorphisms	DR-DQ*03-02	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DQB1	polymorphisms	DR-DQ*07-02	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DQB1	polymorphisms	DR-DQ*03-06	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DQB1	polymorphisms	DR-DQ*15-06	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	A significant increase of DRB1*15 allele frequency and HLA-DRB1*15-DQB1*06 haplotype were observed in Moroccan MS patients.	N/A	23849771	Details
HLA-DQB1	polymorphisms	DR-DQ*01-05	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DQB1	polymorphisms	DR-DQ*03-03	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DQB1	polymorphisms	DR-DQ*11-03	PCR-SSP and/or Luminex (PCR-SSO)	MS	Disease risk	No association of the DR15 allele with sex or age at onset was appreciated. Concerning HLA-DQB1* alleles, no significant difference between patients and controls was found.	N/A	23849771	Details
HLA-DRB1	allele	DRB11501	PCR/SSO	MS	Disease risk	An association was found between PPMS and DRB1*1501 allele.Severe morbidity was found in DRB1*1501-positive PPMS patients. Stratification according to ethnic group showed DRB11501 to be significantly associated with PPMS irrespective of ethnicity.	The heterogeneity found in multiple sclerosis patients with respect to clinical presentation and temporal progression may be a consequence of the complex interaction between the genetic and environmental factors affecting its prevalence, geographical distribution and severity.The effect of HLA alleles on the outcome of the disease has been investigated in several studies;	1961631	Details
HLA-DQB1	allele	DQB10602	PCR/SSO	MS	Disease risk	With respect to the HLA alleles, an association was found between PPMS and DQB10602.	The heterogeneity found in multiple sclerosis patients with respect to clinical presentation and temporal progression may be a consequence of the complex interaction between the genetic and environmental factors affecting its prevalence, geographical distribution and severity.The effect of HLA alleles on the outcome of the disease has been investigated in several studies;	1961631	Details
HLA-DQB1	haplotype	*0602	PCR/SSO	MS	Disease risk	DQB1*0602 was the only allele that maintained an association with MS in a logistic regression model.	The genomic region that codes for the major histocompatibility complex (MHC) has been most consistently associated with MS. The human leukocyte antigens (HLA) class II DR2 haplotype has been associated in varying degrees with MS in all ethnic groups, but particularly strongly in Caucasians.	15083289	Details
CTLA-4	SNP	NA	PCR/TaqMan Assay/multiplex SNaPshot assay	MS	Disease risk	No individual marker or common haplotype showed evidence of association with disease. These data suggest that any effect of CTLA-4 on multiple sclerosis susceptibility is likely to be very small.	V ariation in the cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) gene plays a significant role in determining susceptibility to autoimmune thyroid disease and type 1 diabetes.	16325273	Details
CTLA4	SNP	rs3087243	PCR、SNaPshot	MS	Disease risk	Those MS patients with AA and AG genotypes had 4.36 times greater risk of progressing from the relapsing-remitting to the secondary progressive form of the disease than those with the GG genotype	CTLA-4 antigen molecule plays a key role in the downregulation of T-cell responses	15180809	Details
CD40	SNP	rs1883832CT	PCR、TaqMan SNP Genotyping Assays	MS	Disease risk	we were not able to detect gene-gene interactions between CD40 and CD40L polymorphisms associated with multiple sclerosis.	N/A	24912008	Details
CD40	SNP	rs1883832CC	PCR、TaqMan SNP Genotyping Assays	MS	Disease risk	we were not able to detect gene-gene interactions between CD40 and CD40L polymorphisms associated with multiple sclerosis.	N/A	24912008	Details
CD40	SNP	rs1883832TT	PCR、TaqMan SNP Genotyping Assays	MS	Disease risk	we were not able to detect gene-gene interactions between CD40 and CD40L polymorphisms associated with multiple sclerosis.	N/A	24912008	Details
MIR146A	SNP	rs2910164	PCR–restriction fragment length polymorphism	MS	N/A	Allelic and genotypic associations between the SNPs and MS were evaluated by the data analysis conducted by SPSS V.20. The frequencies of rs2910164 and rs1044165 SNPs were significantly different between the patients with MS and healthy controls. C and T alleles in the variants rs2910164 and rs1044165, respectively, are associated with increased risk of MS. Such association was obtained in codominant, dominant, and overdominant models for both variants (OR ~3 and OR ~1.5, respectively).	microRNAs (miRNAs), are involved in increased or decreased expression of molecules at the onset of MS or through its progression and exacerbation	33478974	Details
MIR223	SNP	rs1044165	PCR–restriction fragment length polymorphism	MS	N/A	Allelic and genotypic associations between the SNPs and MS were evaluated by the data analysis conducted by SPSS V.20. The frequencies of rs2910164 and rs1044165 SNPs were significantly different between the patients with MS and healthy controls. C and T alleles in the variants rs2910164 and rs1044165, respectively, are associated with increased risk of MS. Such association was obtained in codominant, dominant, and overdominant models for both variants (OR ~3 and OR ~1.5, respectively).	microRNAs (miRNAs), are involved in increased or decreased expression of molecules at the onset of MS or through its progression and exacerbation	33478974	Details
MMP9	Allele	NA	PCR–RFLP	MS	Disease risk	The MMP-2 polymorphism led to a 5-year-earlier age of disease onset in MS patients with ON as a first symptom (p = 0.009).	N/A	26298319	Details
MMP2	Allele	NA	PCR–RFLP	MS	Disease risk	The MMP-2 polymorphism led to a 5-year-earlier age of disease onset in MS patients with ON as a first symptom (p = 0.009).	N/A	26298319	Details
TNF	SNP	—308 polymorphism	Polymerase chain reaction (PCR) amplification,Polymerase chain reaction (PCR) amplification. Allele-specific PCR.	MS	Phenotypic risk	We studied the association of the two most common mutations with the mean ranked severity score and with the temporal profile of MS in patients with available clinical information.No association was evident.An analysis of the distribution of severity scores and a linear regression analysis of EDSS according to duration did not reveal any differences between those with the variants and the wild-type sequence.	N/A	9270565	Details
HLA-DRB1	DRB1*1501	N/A	polymerase chain reaction and sequence-specific oligonucleotide probe hybridization	MS	Disease risk	The haplotype DRB1*1501, DQA1*0102, DQB1*0602 was found to be associated with MS among both Ashkenazi and non-Ashkenazi patients (P<.001 and P =.04, respectively).	N/A	10328250	Details
HLA-DQA1	DQA1*0102	N/A	polymerase chain reaction and sequence-specific oligonucleotide probe hybridization	MS	Disease risk	The haplotype DRB1*1501, DQA1*0102, DQB1*0602 was found to be associated with MS among both Ashkenazi and non-Ashkenazi patients (P<.001 and P =.04, respectively).	N/A	10328250	Details
HLA-DQB1	DQB1*0602	N/A	polymerase chain reaction and sequence-specific oligonucleotide probe hybridization	MS	Disease risk	The haplotype DRB1*1501, DQA1*0102, DQB1*0602 was found to be associated with MS among both Ashkenazi and non-Ashkenazi patients (P<.001 and P =.04, respectively).	N/A	10328250	Details
TNF	polymorphisms	N/A	polymorphism of TNF-α microsatellite	MS	Disease risk	The frequencies of TNF-α*11 and TNF-α*10 alleles increased in patients with MS compared with controls, showing a significant difference among the studied population.	N/A	25763268	Details
IL2RA	SNP	rs12722489,rs2104286	population-based cohort, restriction fragment length polymorphism (RFLP) following polymerase chain reaction (PCR) amplification	MS	Disease risk	rs12722489 and rs2104286 were not in linkage disequilibrium with each other in cases or controls. We did not find association between haplotypes, genotypes or alleles of rs12722489 and rs21042861 and susceptibility to MS in our populationbased sample. There was no association with disease severity and no gender-dependent effect.	N/A	21239413	Details
WT1	SNP	rs10767935, rs5030244	predesigned Taqman SNP genotyping assays	MS	Treatment risk	In this prospective study with repeated measurements of 25-hydroxyvitamin D before and during treatment with IFN-β, we did not find that genetic variation in WT1 plays any role in regulating the relationship between IFN-β and serum 25-hydroxyvitamin D.	High serum levels of vitamin D have been shown to be associated with low risk of developing multiple sclerosis (MS) and are also associated with low clinical and radiological disease activity . IFN-b treatment was associated with reduced relapse risk only in patients with serum 25(OH)D above 50 nmol/l, suggesting that the effect of IFN-b was mediated through 25(OH)D.	26037530	Details
HLA-DPA1	polymorphism	HLA-DPw4	Primed Lymphocyte Typing, RFLP	MS	Disease risk	HLA-DPw4 was found in 93.3% of MS patients compared to 72.3% of controls.DPw4 seems to confer susceptibility to MS independently .	The genetic susceptibility to multiple sclerosis (MS) is at least partly controlled by one or more genes in the class â…¡ region of the HLA system.	3400089	Details
HLA-DRB1	polymorphism	HLA-DR2	Primed Lymphocyte Typing, RFLP	MS	Disease risk	DR2 was found in 75.5% of MS patients compared to 33.7% of controls.DR2 seems to confer susceptibility to MS independently .	The genetic susceptibility to multiple sclerosis (MS) is at least partly controlled by one or more genes in the class â…¡ region of the HLA system.	3400089	Details
NECTIN2	SNP	rs394221	Public domain databases and SNPSelector were used to identify SNPs from the following five plausible MS candidate genes.Monks—Kaplan quantitative transmission/disequilibrium test (MK-QTDT)	MS	Disease risk	showed significant evidence for an association with MS severity.	N/A	16738668	Details
HLA-DRB1	DNA methylation at CpG dinucleotides	N/A	pyrosequencing,RT-PCR	MS	Phenotypic risk	We found no significant effect of DNA methylation across HLA-DRB1*1501 on severity.	N/A	20394989	Details
HLA-DRB5	DNA methylation at CpG dinucleotides	N/A	pyrosequencing,RT-PCR	MS	Phenotypic risk	We found no significant effect of DNA methylation across HLA-DRB5 on severity.	N/A	20394989	Details
IFNG	SNP	rs2069727	qPCR	MS	Disease risk	IFNG is associated with sex bias in MS susceptibility and with expression of IFN gamma in MS	an interaction between sex andIFNgamma expression in a variety of disease states	18332247	Details
STAT3	methylation	N/A	qPCR	MS	Disease risk	Our study demonstrated that the level of STAT3 methylation decreased in relapsing–remitting MS patient compared to control groups, which the decreases were statistically signifcant.	signal transducer and activator of transcription 3 (STAT3) play a critical role in the induction of Th17 cell diferentiation and inhibition of Treg cell development.	33375941	Details
LMNB1	Allele	NA	qPCR	MS	Disease risk	Our work indicates that lamin B1 defects are probably not responsible for signs and symptoms resembling multiple sclerosis.	Whole gene duplication of the lamin B1 gene (LMNB1), encoding for a protein of the nuclear lamina, causes an adult-onset autosomal dominant leukodys-trophy (ADLD).	19348623	Details
CIITA	SNP	rs3087456	qPCR	MS	Disease risk	We then analyzed the combinations of genotypes formed by those two markers, which were in moderate linkage disequilibrium in our population, and multivariate analysis suggested that it depended more on rs4774 than on rs3087456.	N/A	17678724	Details
CIITA	SNP	rs4774	qPCR	MS	Disease risk	We then analyzed the combinations of genotypes formed by those two markers, which were in moderate linkage disequilibrium in our population, and multivariate analysis suggested that it depended more on rs4774 than on rs3087456.	This would result in viral activation that in turn might underlie some cases of MS.	17678724	Details
VMP1	SNP	RS8070345	qPCR	MS	Phenotypic risk	We observed significant methylation differences in the VMP1/MIR21 locus, with RR-MS dis-playing higher methylation compared to SP-MS and HC.	Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system caused by genetic and environmental factors. DNA methylation, an epigenetic mechanism that controls genome activity, may provide a link between genetic and environmental risk factors.	28766461	Details
VMP1	SNP	RS8070345	qPCR	MS	Disease risk	VMP1/MIR21 methylation did not correlate with a known MS risk variant in VMP1 or smoking but displayed a significant negative correlation with age and the levels of mature miR-21 in CD4+ T cells	Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system caused by genetic and environmental factors. DNA methylation, an epigenetic mechanism that controls genome activity, may provide a link between genetic and environmental risk factors.	28766461	Details
SP140	SNP	rs28445040	qPCR	MS	Disease risk	rs28445040 variant was the causal factor for skipping of exon 7.	N/A	26152201	Details
NINJ2	SNP	rs7298096	qPCR	MS	Treatment risk	The distribution of rs7298096 SNP was significantly different in the responders and non-responder patients and the NINJ2 gene expression considerably increased in the non-responder patients compare to the responders.The NINJ2 gene expression level in the AA genotype of the non-responder group was higher than to the other genotypes of both groups.	According to a genomewide association study (GWAS) with 4-year follow-up that performed on RRMS patients, the rs7298096 polymorphism in the NINJ2 gene was shown the strong association with IFN-β response.The NINJ2 encodes for Ninjurin-2 protein, which is a cell surface adhesion protein, and as its paralogue, NINJ1 plays a role in nerve regeneration, inflammation, and endothelial cell activation.	35912872	Details
CD58	SNP	rs2300747 A>G	qPCR	MS	Disease risk	Concerning rs2300747 polymorphism on CD58 gene, no significant differences were found between cases and controls	genome-wide association studies have identified susceptibility of immune-related genes to be involved in MS predisposition	30128676	Details
CD226	SNP	rs763361 C>T	qPCR	MS	Disease risk	Our finding showed that there are significant differences in genotype and allele frequencies between two groups regarding rs763361 (P = 0.035, OR 0.64, CI 95% for C allele) and rs1611715 (P = 0.038, OR 1.57, CI 95% for AA genotype) polymorphisms within CD226 and HLA-G genes	genome-wide association studies have identified susceptibility of immune-related genes to be involved in MS predisposition	30128676	Details
HLA-G	SNP	rs1611715 A>C	qPCR	MS	Disease risk	Our finding showed that there are significant differences in genotype and allele frequencies between two groups regarding rs763361 (P = 0.035, OR 0.64, CI 95% for C allele) and rs1611715 (P = 0.038, OR 1.57, CI 95% for AA genotype) polymorphisms within CD226 and HLA-G genes	genome-wide association studies have identified susceptibility of immune-related genes to be involved in MS predisposition	30128676	Details
CYP2R1	SNP	rs10766197	qPCR	MS	Disease risk	Carriers of GA + AA genotypes of CYP2R1 rs10766197 had an increased risk of MS	Low vitamin D levels have been reported to be a risk factor for MS, and genetic variances could be implicated	34977256	Details
CYP27B1	SNP	rs10877012	qPCR	MS	Disease risk	No differences were observed in the frequency of T allele of CYP27B1 rs10877012ï¼›No increased risk was observed in GT + TT genotypes of CYP27B1 rs10877012	Low vitamin D levels have been reported to be a risk factor for MS, and genetic variances could be implicated	34977256	Details
Galc	mutation	GALC +/-	qPCR	EAE	Disease risk	thus provide a potential functional link between GALC variants and increased MS susceptibility, particularly due to the failure of remyelination associated with progressive MS.	N/A	28575206	Details
NOS3	SNP	rs2070744	qPCR	MS	Disease risk	The frequencies of rs2070744 genotypes and allelic variants were not associated with the risk of developing MS and were not infuenced by gender, age at onset and severity of MS, the clinical subtype of MS or the HLA-DRB1*1501 genotype.	N/A	32449012	Details
IL7R	SNP	rs6897932	QPCR	MS	Disease risk	In particular, homozygosity for the risk allele is a risk factor for MS in our population (ORCC vs CT and TT 1.65 (95% CI: 1.18–2.30), two-sided p 0.004). However, no effect of genotype or the relative expression of membrane-bound IL7R (presence of exon 6–7) to total amount of IL7R mRNA (presence of exon 4–5) was found on MS phenotype.	The interleukin 7 receptor (IL7R) has been recognized as a susceptibility gene for Multiple Sclerosis (MS). Analysis of rs6897932 (the most strongly MS-associated single nucleotide polymorphism (SNP)), showed effects of genotype on the relative expression of membrane-bound to total amount of IL7R mRNA.	21543551	Details
HLA-DRB1	SNP	HLA-DRB1*15+/-	qPCR	MS	Disease risk	The relationship between HLA alleles and viral parameters was exclusively seen in MS patient.MS patients carrying the HLA-DRB1*15 allele (HLA-DRB1*15+) (N = 42/117) had higher EBV viral load than those not carrying this allele (HLA-DRB1*15) .The highest EBV viral load was detected in HLA-B*07+/HLA-DRB1*15+/HLA-A*02 (least favorable HLA combination) patients;the 25 HLA-B*07/HLA-DRB1*15/HLA-A*A02+ patients were characterized by the lowest EBV viral load.	HLA-class I molecules present antigens to T lymphocytes and initiate immune response against viruses.	29587799	Details
HLA-A	SNP	HLA-A*02+/-	qPCR	MS	Disease risk	The relationship between HLA alleles and viral parameters was exclusively seen in MS patient.A significantly lower EBV viral load was observed in MS patients expressing the HLA-A*02 antigen (HLA-A*02+) , which is suggested to be a protective factor in MS, compared to those without the allele (HLA-A*02).The highest EBV viral load was detected in HLA-B*07+/HLA-DRB1*15+/HLA-A*02 (least favorable HLA combination) patients;the 25 HLA-B*07/HLA-DRB1*15/HLA-A*A02+ patients were characterized by the lowest EBV viral load.	N/A	29587799	Details
HLA-B	SNP	HLA-B*07+/-	qPCR	MS	Disease risk	The relationship between HLA alleles and viral parameters was exclusively seen in MS patient.A significantly higher EBV viral load could be detected in MS subjects carrying the HLA-B*07 allele (HLA-B*07+)compared to those not carrying this allele (HLA-B*07).The highest EBV viral load was detected in HLA-B*07+/HLA-DRB1*15+/HLA-A*02 (least favorable HLA combination) patients;the 25 HLA-B*07/HLA-DRB1*15/HLA-A*A02+ patients were characterized by the lowest EBV viral load.	N/A	29587799	Details
IKZF3	SNP	rs907091	qPCR,online tools SNAP	MS	Disease risk	The transcript of the haplotype containing the MS risk allele at rs907091 in IKZF3, showed consistently higher expression level in all MS samples.Consistent allelic imbalance is observed for rs907091 in IKZF3. The studied SNP in IKZF3 is located in a cis-regulatory element, or that these SNPs mark a functional cis-regulatory element that impacts the per-allele transcript abundance in whole blood, independent of disease status.	N/A	27080863	Details
CD69	SNP	rs11052877	qPCR,online tools SNAP	MS	Disease risk	There is no consistent cis-regulatory mechanism for CD69 associated with this SNP.	N/A	27080863	Details
IQGAP1	SNP	rs11609	qPCR,online tools SNAP	MS	Disease risk	The transcript of the haplotype containing the MS risk allele at rs11609 in IQGAP1 was higher in the majority of MS samples.Consistent allelic imbalance is observed for rs11609 in IQGAP1.The studied SNP IQGAP1 is located in a cis-regulatory element, or that these SNPs mark a functional cis-regulatory element that impacts the per-allele transcript abundance in whole blood, independent of disease status. Given this observation, a relative higher expression of IQGAP1 for carriers of the minor allele might contribute to an increase in MS susceptibility.	N/A	27080863	Details
HLA-DRB1	SNP	rs3135388	qRT‐PCR	MS	Disease risk	The results show that only two patients with the HLA‐HLA‐DRB1*13 allele and three with the HLA-DRB1*15 allele carried the specific variant in heterozygosis (A/G).All individuals, either patients or controls carrying the HLA‐DRB1*11 allele, had the nonrisk GG genotype.	In multiple sclerosis, the disease‐associated HLA‐DR heterodimers play a pivotal role in presenting immunogenic peptides from myelin proteins to pathogenic CD4+ T cells.	31313885	Details
LINE-1	methylation	N/A	Quantitative PCR	MS	Disease risk	The methylation level of L1PA2 CpG site 10 was significantly and negatively correlated with the EDSS score (the correlation coefficient is 0.69, p = 0.004).	N/A	28707075	Details
IL18R1	N/A	rs7579737	Quantitative real-time PCR	MS	Disease risk	using 13 tagging single nucleotide polymorphisms (SNPs) across the IL18R1 gene, but determined no SNP or haplotype association	The interleukin 18 receptor 1 (IL18R1) was recently identified to regulate experimental autoimmune	20354066	Details
IL18R1	N/A	rs7558013	Quantitative real-time PCR	MS	Disease risk	using 13 tagging single nucleotide polymorphisms (SNPs) across the IL18R1 gene, but determined no SNP or haplotype association	The interleukin 18 receptor 1 (IL18R1) was recently identified to regulate experimental autoimmune	20354066	Details
IL18R1	N/A	rs2241116	Quantitative real-time PCR	MS	Disease risk	using 13 tagging single nucleotide polymorphisms (SNPs) across the IL18R1 gene, but determined no SNP or haplotype association	The interleukin 18 receptor 1 (IL18R1) was recently identified to regulate experimental autoimmune	20354066	Details
IL18R1	N/A	rs17027056	Quantitative real-time PCR	MS	Disease risk	using 13 tagging single nucleotide polymorphisms (SNPs) across the IL18R1 gene, but determined no SNP or haplotype association	The interleukin 18 receptor 1 (IL18R1) was recently identified to regulate experimental autoimmune	20354066	Details
IL18R1	N/A	rs4851005	Quantitative real-time PCR	MS	Disease risk	using 13 tagging single nucleotide polymorphisms (SNPs) across the IL18R1 gene, but determined no SNP or haplotype association	The interleukin 18 receptor 1 (IL18R1) was recently identified to regulate experimental autoimmune	20354066	Details
IL18R1	N/A	rs6706002	Quantitative real-time PCR	MS	Disease risk	using 13 tagging single nucleotide polymorphisms (SNPs) across the IL18R1 gene, but determined no SNP or haplotype association	The interleukin 18 receptor 1 (IL18R1) was recently identified to regulate experimental autoimmune	20354066	Details
IL18R1	N/A	rs11465597	Quantitative real-time PCR	MS	Disease risk	using 13 tagging single nucleotide polymorphisms (SNPs) across the IL18R1 gene, but determined no SNP or haplotype association	The interleukin 18 receptor 1 (IL18R1) was recently identified to regulate experimental autoimmune	20354066	Details
IL18R1	SNP	rs10515921	Quantitative real-time PCR	MS	Disease risk	using 13 tagging single nucleotide polymorphisms (SNPs) across the IL18R1 gene, but determined no SNP or haplotype association	The interleukin 18 receptor 1 (IL18R1) was recently identified to regulate experimental autoimmune	20354066	Details
IL18R1	SNP	rs7603730	Quantitative real-time PCR	MS	Disease risk	using 13 tagging single nucleotide polymorphisms (SNPs) across the IL18R1 gene, but determined no SNP or haplotype association	The interleukin 18 receptor 1 (IL18R1) was recently identified to regulate experimental autoimmune	20354066	Details
IL18R1	SNP	rs6750020	Quantitative real-time PCR	MS	Disease risk	using 13 tagging single nucleotide polymorphisms (SNPs) across the IL18R1 gene, but determined no SNP or haplotype association	The interleukin 18 receptor 1 (IL18R1) was recently identified to regulate experimental autoimmune	20354066	Details
IL18R1	SNP	rs3213733	Quantitative real-time PCR	MS	Disease risk	using 13 tagging single nucleotide polymorphisms (SNPs) across the IL18R1 gene, but determined no SNP or haplotype association	The interleukin 18 receptor 1 (IL18R1) was recently identified to regulate experimental autoimmune	20354066	Details
IL18R1	SNP	rs2041740	Quantitative real-time PCR	MS	Disease risk	using 13 tagging single nucleotide polymorphisms (SNPs) across the IL18R1 gene, but determined no SNP or haplotype association	The interleukin 18 receptor 1 (IL18R1) was recently identified to regulate experimental autoimmune	20354066	Details
IL18R1	SNP	rs11903946	Quantitative real-time PCR	MS	Disease risk	using 13 tagging single nucleotide polymorphisms (SNPs) across the IL18R1 gene, but determined no SNP or haplotype association	The interleukin 18 receptor 1 (IL18R1) was recently identified to regulate experimental autoimmune	20354066	Details
Gria3	Deletion	N/A	quantitative reverse transcriptase-PCR	EAE	Disease risk	Disruption of the Gria3 gene did not induce compensatory changes in levels of mRNAs encoding GluR1, GluR2, or GluR4 in mouse spinal cord or cerebellum, but GluR1 mRNA was significantly elevated in Gria3 mutant cerebral cortex.GluR2-free AMPA receptor-mediated currents are markedly diminished in Gria3-deficient OLC.Whole-cell capacitances of Gria3 mutant and control OLC, did not differ significantly.Block of AMPA receptor currents by NASPM is less in Gria3 mutant (Gria3 KO) than in wild-type (WT) control OLC. OLC from Gria3 mutant mice was less susceptible than control OLC to excitotoxic death.Experimental autoimmune encephalomyelitis clinical deficits and spinal cord demyelination are less severe in Gria3 mutant mice than in wild-type littermate controls.	This use-dependence has been attributed to a greater accessibility of the polyamine toxin to its interaction site in the agonist-bound, open state of GluR2-lacking AMPA receptors, resulting in an attenuated initial response shortened and further attenuated by the progressive block by the toxin as it enters the opened pores of the channels.OLC excitotoxicity mediated by GluR2-free, Ca2+- permeable AMPA receptors contributes substantially to clinical deficits and demyelination in EAE.	17472701	Details
Qki	polymorphisms	V1	quantitative RT-PCR	EAE	Disease risk	Decreased expression of mice QKI –V1 (equivalent to human QKI -V5)in the brain of EAE mice	N/A	31835207	Details
HLA-DRB1	haplotype	HLA-DRB1*15:01 haplotype	Real Time PCR	MS	Disease risk	Our data confirms that the *15:01 haplotype confers a higher risk of suffering from MS. Sex confers a much stronger modulation and the *15:01-MS association seems to be female specific.	The pathogenic mechanisms of the disease are not yet clearly identified; however, one proposal is an activation of the lymphocytes that cross the blood–brain barrier (BBB) directly into the interstitial matrix. T cells are then reactivated by fragments of the myelin antigens exposed in the context of human leukocyte antigen (HLA) molecules of the surface of the antigen presenting cells.	22127897	Details
IGH	CNV	VH4-34 genecopy number	Real Time PCR	MS	Disease risk	MS patients had significantly lower VH4-34 gene copy number levels compared to the control group.	Natural IgM (nIgM) antibodiesregulate the immune system against autoantigens andare essential for maintaining tissue homeostasis.The anti-inflammatory actions of B1 cells include the generation of nIgM bythe spleen and bone marrow as a primary response to pathogen invasions,the removal of necrotic and apoptotic cells,the maintenance of tissue homeostasis the reductionof inflammatory cytokines, and enhanced release of GcMAF. SeveralVH genes encode natural antibodies, but the VH4-34 gene appears to be the most common.An interesting featureis that the framework region 1 (FWR1) mediates self-antigen binding,and the VH4-34 gene is essentialfor encoding nIgM.	36640058	Details
LAG3	SNP	rs870849	Real Time PCR	MS	Disease risk	The frequencies of the LAG3 rs878049 genotypes and allelic variants that were in the Hardy–Weinberg equilibrium, both in MS patients and in controls, did not differ significantly between the two study groups when comparing the whole series and when analyzed each gender separately.	LAG3 protein is encoded by the lymphocyte activation gene 3 (LAG3). This protein is expressed by regulatory T cells, both activated and exhausted CD4+ and CD8+ T cells, and microglia, and its main mechanism of action is to deliver inhibitory signals that are involved in the regulation of immune cell homeostasis, T cell activation and proliferation, production of cytokines, cytolytic activity, and other functions related to inflammatory responses.	36499569	Details
CD4	SNP	rs1922452	Real Time PCR	MS	Disease risk	The frequencies of the CD4 rs1992452 genotypes and allelic variants that were in the Hardy–Weinberg equilibrium, both in MS patients and in controls, did not differ significantly between the two study groups when comparing the whole series and when analyzed each gender separately.	The CD4 molecule gene which is closely related to the LAG3 gene, encodes the CD4 membrane glycoprotein of T lymphocytes. This glycoprotein is also an important mediator of immune and inflammatory responses.	36499569	Details
CD4	SNP	rs951818	Real Time PCR	MS	Disease risk	The frequencies of the CD4 rs951818 genotypes and allelic variants that were in the Hardy–Weinberg equilibrium, both in MS patients and in controls, did not differ significantly between the two study groups when comparing the whole series and when analyzed each gender separately.	The CD4 molecule gene which is closely related to the LAG3 gene, encodes the CD4 membrane glycoprotein of T lymphocytes. This glycoprotein is also an important mediator of immune and inflammatory responses.	36499569	Details
IL7R	SNP	504 C (GCA haplotype)	Real Time PCR	MS	Disease risk	In the case control study, there was over-representation of the 504 T allele in PPMS and a non-significant trend towards over-representation of the C allele in SPMS.In healthy controls, no difference in promoter haplotype expression was detected, but in CPMS patients, a small but significant difference was detected in haplotype expression, with promoter haplotype GCA being the high expressor.	N/A	16075257	Details
APOE	DNA methylation	N/A	real time PCR	MS	N/A	The data indicate that the increase in expression of ACKR3 gene by hypomethylation and the decrease in expression of APOE gene via hypermethylation are possibly involved in the onset and progression of inflammatory processes in MS patients.	the methylation pattern of these genes can be involved in the onset and/or progression of inflammatory processes in MS.	34624384	Details
ACKR3	DNA methylation	N/A	real time PCR	MS	N/A	The data indicate that the increase in expression of ACKR3 gene by hypomethylation and the decrease in expression of APOE gene via hypermethylation are possibly involved in the onset and progression of inflammatory processes in MS patients.	the methylation pattern of these genes can be involved in the onset and/or progression of inflammatory processes in MS.	34624384	Details
IL-1RL1	SNP	rs10204137	real time PCR	MS	Disease risk	The frequency distribution of the genotype in rs10204137 variant of IL-33 gene in MS patients and healthy subjects was significantly different (p = 0.013).	N/A	30950351	Details
IL33	SNP	rs1342326(TT)	real time PCR	MS	Disease risk	The frequency distribution of the genotype in rs1342326 variant of IL-33 gene in patients with asthma, MS and healthy subjects was not significantly different (P>0.05).	N/A	30950351	Details
QKI	polymorphisms	V5	Real time RT-PCR	MS	Disease risk	Decreased expression of QKI -V5 in peripheral blood of patients with multiple sclerosis (MS)	N/A	31835207	Details
Qki	polymorphisms	V5	Real time RT-PCR	EAE	Disease risk	The blood and brain of EAE mice exhibited a corresponding decrease in QKI-V5 expression.	N/A	31835207	Details
Nmnat2	overexpression	N/A	real-time PCR	EAE	Disease risk	NMNAT2 activation in RGCs does not provide significant neuroprotection of RGCs in EAE/optic neuritis.	N/A	34707482	Details
HLA-G	Insertion	14bp	Real-Time PCR	MS	Phenotypic risk	In particular,there was a significant difference among the distinct combined HLA-G genotypes for serum sHLA-G concentrations in both MRI inactive and active RR-MS patientsas well as for CSF sHLA-G values in RR-MS patients with MRI inactive and active disease.The highest serum and CSF sHLA-G levels predominated in MRI inactive and active RR-MS patients with C/C,DEL/DEL genotype, who can be judged as the "true" high HLA-G producers.In contrast, the lowest serum and CSF sHLA-G titers prevailed in MRI inactive and active RR-MS patients with G/G,INS/INS who can be accepted as the "true" low sHLA-G producers.	A growing body of evidence has indicated a possible involvement of HLA (Human Leukocyte Antigen)-G antigens in MS where this molecule seems to exhibit antinflammatory properties.HLA-G is characterized by tolerogenic functions, inducing apoptosis of activated CD8+ T cells , acting on T regulatory cells , modulating the activity of natural killer cells and of dendritic cells and blocking allo-cytotoxic T lymphocyte response.These immuno-regulatory functions are mediated by the interaction of HLA-G molecules with specific inhibitory receptors.HLA-G is currently believed to play a tolerogenic role in the regulation of MS autoimmunity.	22922127	Details
HLA-G	Deletion	14bp	Real-Time PCR	MS	Phenotypic risk	In particular,there was a significant difference among the distinct combined HLA-G genotypes for serum sHLA-G concentrations in both MRI inactive and active RR-MS patientsas well as for CSF sHLA-G values in RR-MS patients with MRI inactive and active disease.The highest serum and CSF sHLA-G levels predominated in MRI inactive and active RR-MS patients with C/C,DEL/DEL genotype, who can be judged as the "true" high HLA-G producers.In contrast, the lowest serum and CSF sHLA-G titers prevailed in MRI inactive and active RR-MS patients with G/G,INS/INS who can be accepted as the "true" low sHLA-G producers.	A growing body of evidence has indicated a possible involvement of HLA (Human Leukocyte Antigen)-G antigens in MS where this molecule seems to exhibit antinflammatory properties.HLA-G is characterized by tolerogenic functions, inducing apoptosis of activated CD8+ T cells , acting on T regulatory cells , modulating the activity of natural killer cells and of dendritic cells and blocking allo-cytotoxic T lymphocyte response.These immuno-regulatory functions are mediated by the interaction of HLA-G molecules with specific inhibitory receptors.HLA-G is currently believed to play a tolerogenic role in the regulation of MS autoimmunity.	22922127	Details
HLA-G	polymorphism	+3142C>G	Real-Time PCR	MS	Phenotypic risk	In particular,there was a significant difference among the distinct combined HLA-G genotypes for serum sHLA-G concentrations in both MRI inactive and active RR-MS patientsas well as for CSF sHLA-G values in RR-MS patients with MRI inactive and active disease.The highest serum and CSF sHLA-G levels predominated in MRI inactive and active RR-MS patients with C/C,DEL/DEL genotype, who can be judged as the "true" high HLA-G producers.In contrast, the lowest serum and CSF sHLA-G titers prevailed in MRI inactive and active RR-MS patients with G/G,INS/INS who can be accepted as the "true" low sHLA-G producers.	A growing body of evidence has indicated a possible involvement of HLA (Human Leukocyte Antigen)-G antigens in MS where this molecule seems to exhibit antinflammatory properties.HLA-G is characterized by tolerogenic functions, inducing apoptosis of activated CD8+ T cells , acting on T regulatory cells , modulating the activity of natural killer cells and of dendritic cells and blocking allo-cytotoxic T lymphocyte response.These immuno-regulatory functions are mediated by the interaction of HLA-G molecules with specific inhibitory receptors.HLA-G is currently believed to play a tolerogenic role in the regulation of MS autoimmunity.	22922127	Details
CLEC16A	SNP	rs7206912,rs6498168,rs9934231,rs6498169,rs8060411	real-time PCR	MS	Disease risk	In the Norwegian replication sample set, all SNPs except rs12923849 were replicated to be associated at the 5% significance level, with rs7296012 being the most strongly associated.	The association of CLEC16A SNPs across multiple immune-mediated diseases and the observation that the gene is almost uniquely expressed on immune cells, make a common effect on autoimmunity likely.The CLEC16A protein belongs to the C-type lectin family whose immune functions include differentiation of self versus non-self glycoproteins and the induction of the appropriate immune response.	21179112	Details
CLEC16A	SNP	rs12708716 , rs12923849	real-time PCR	MS	Disease risk	In the UK replication sample set, rs12708716 and rs12923849 were significantly associated in the trios and case controls combined.	The association of CLEC16A SNPs across multiple immune-mediated diseases and the observation that the gene is almost uniquely expressed on immune cells, make a common effect on autoimmunity likely.The CLEC16A protein belongs to the C-type lectin family whose immune functions include differentiation of self versus non-self glycoproteins and the induction of the appropriate immune response.	21179112	Details
IL7R	SNP	rs6897932	real-time PCR	MS	Disease risk	The frequencies of both the C allele and the CC genotype of SNP rs6897932 in the IL-7RA gene in patients with non-NMO MS were significantly higher than those of HCs.However, there was no significant difference in the frequency of either the C allele or the CC genotype between HCs and patients with NMO. The frequencies of both the C allele and the CC genotype were significantly higher in patients with CMS than in HCs, but not in patients with OSMS. This study revealed a significant association of the SNP rs6897932 of IL-7RA gene with non-NMO MS in Japanese populations.	The SNP located in the transmembrane domain of IL-7Rα is nonsynonymous and functional: the MS-susceptible CC allele increases levels of the soluble form of IL-7Rα via exon skipping, and decreases the expression of membranebound IL-7Rα, thereby causing decreased IL-7/ IL-7R signaling.IL-7/IL-7R signaling induces thymic production of FOXP3 regulatory T cells, which efficiently ameliorate experimental autoimmune encephalomyelitis,an animal model of MS.	21670443	Details
LEP	SNP	rs11761556,rs2167270,rs7799039	real-time PCR	MS	Disease risk	Allele and genotype frequencies did not differ significantly between MS patients and controls.	Leptin also plays an important role in the regulation of immune responses and pro-inflammatory cytokine secretion.It binds to the leptin receptor (LEPR), which belongs to the class I cytokine receptor superfamily and acts through the classical JAK-STAT pathway.	21664965	Details
LEPR	SNP	rs1137100,rs1137101,rs8179183	real-time PCR	MS	Disease risk	Allele and genotype frequencies did not differ significantly between MS patients and controls.	Leptin also plays an important role in the regulation of immune responses and pro-inflammatory cytokine secretion.It binds to the leptin receptor (LEPR), which belongs to the class I cytokine receptor superfamily and acts through the classical JAK-STAT pathway.	21664965	Details
GHRL	SNP	rs696217,rs1629816,rs4684677	real-time PCR	MS	Disease risk	Allele and genotype frequencies did not differ significantly between MS patients and controls.	Through binding to the growth hormone secretagogue receptor (GHSR), ghrelin is involved in the regulation of energy homeostasis and has also been shown to inhibit inflammatory processes.	21664965	Details
GHSR	SNP	rs519384,rs509035,rs5772169	real-time PCR	MS	Disease risk	Allele and genotype frequencies did not differ significantly between MS patients and controls.	Through binding to the growth hormone secretagogue receptor (GHSR), ghrelin is involved in the regulation of energy homeostasis and has also been shown to inhibit inflammatory processes.	21664965	Details
CD58	SNP	rs12044852	real-time PCR	MS	Disease risk	Association (allelic model) between multiple sclerosis and CD58 gene polymorphism alleles rs12044852 (p=0.410), rs2300747 (p=0.881) and rs1335532 (p=0.407) were indistinct.	CD58 gene is located on chromosome one and it encodes a member of the T lymphocytes CD2 protein ligand	32257069	Details
CD58	SNP	rs2300747	real-time PCR	MS	Disease risk	Association (allelic model) between multiple sclerosis and CD58 gene polymorphism alleles rs12044852 (p=0.410), rs2300747 (p=0.881) and rs1335532 (p=0.407) were indistinct.	CD58 gene is located on chromosome one and it encodes a member of the T lymphocytes CD2 protein ligand	32257069	Details
CD58	SNP	rs1335532	real-time PCR	MS	Disease risk	Association (allelic model) between multiple sclerosis and CD58 gene polymorphism alleles rs12044852 (p=0.410), rs2300747 (p=0.881) and rs1335532 (p=0.407) were indistinct.	CD58 gene is located on chromosome one and it encodes a member of the T lymphocytes CD2 protein ligand	32257069	Details
CCL20	SNP	rs6749704	real-Time PCR	MS	Disease risk	Frequencies of CT genotype of rs6749704 in CCL20 gene and C allele in MS patients were significantly higher compared to controls.	The migration of auto reactive T cells from circulation into the CNS across the (BBB) is a crucial step in the development of pathological lesions in MS, the recruitment of inflammatory cells is controlled by chemokines.CCL20–CCR6 interaction participates in BBB disruption and the subsequent transmigration of pathogenic T cell into the CNS.Moreover, secretion of IL-17 from circulating Th17 cells amplifies the proinflammatory response by enhancing CCL20 transcription via NFkB signaling.	30399422	Details
IL17F	SNP	rs763780	real-Time PCR	MS	Disease risk	Significant increase of rs763780 in IL-17F gene was detected in MS patients.	IL-17 is correlated with disease activity and promote blood-brain barrier (BBB) disruption and CNS inflammation.The IL-17F 7488T/C polymorphism (rs763780) causes an amino acid substitution from histamine to arginine at codon 161 (H161R), in the third exon of the IL17F gene.	30399422	Details
FTO	SNP	rs9939609	Real-time PCR	MS	Disease risk	FTO rs9939609 genotype distribution in the MS cohort did not differ from the sampled healthy Kuwaiti population distributions after adjusting for both age and gender under both an additive and recessive genetic model.	The FTO is an alpha-ketoglutarate dependent dioxygenase that is highly expressed in the nucleus.It is reported to be an RNA demethylase that mediates demethylation of different RNA species including mRNAs, tRNAs and snRNAs.	31836807	Details
VDR	polymorphisms	Taq I (rs731236)	Real-Time PCR	MS	Disease risk	We observed a significant difference between controls and patient group only in Taq I polymorphism (p: 0.025).	Specific variants of the VDR gene are associated with alterations in vitamin D function and metabolism	29416220	Details
FTO	SNP	rs9939609	Real-time PCR	MS	Phenotypic risk	The A-allele was found to be associated with increased MS disability.	The FTO is an alpha-ketoglutarate dependent dioxygenase that is highly expressed in the nucleus.It is reported to be an RNA demethylase that mediates demethylation of different RNA species including mRNAs, tRNAs and snRNAs.	31836807	Details
VDR	polymorphisms	Fok I (rs2228570)	Real-Time PCR	MS	Disease risk	There were no significant association for the Apa I and Fok I polymorphisms.	Specific variants of the VDR gene are associated with alterations in vitamin D function and metabolism	29416220	Details
VDR	polymorphisms	Apa I(rs7975232)	Real-Time PCR	MS	Disease risk	There were no significant association for the Apa I and Fok I polymorphisms.	Specific variants of the VDR gene are associated with alterations in vitamin D function and metabolism	29416220	Details
NQO1	polymorphism	C609 T	Real-Time PCR	MS	Disease risk	The frequencies of variant NQO1 genotypes were significantly higher in MS cases as compared to the controls.Similarly, the T allele frequency was increased in MS patients.	Germline polymorphisms of detoxification genes could influence susceptibility to Multiple Sclerosis (MS).NAD(P)H:quinone oxidoreductase 1 (NQO1) is detoxifying enzymes involved in biotransformation of metabolites preventing cells from oxidative damage.	24588223	Details
HAMP	SNP	rs10421768	Real-time PCR	MS	Phenotypic risk	A statistical trend has been shown regarding the tendency to occur primary relapses more frequently among persons with the AA + AG genotype compared with GG patients in the recessive HAMP rs10421768 inheritance model.	The mechanism of iron regulation in the cell by HAMP is mainly based on the control of FPN expression at the level of its translation.The presence of polymorphisms in the genes of iron metabolism may modulate iron deposition in the body and thus affect the clinical course of the disease.	35682458	Details
USP18	SNP	rs2542109	real-time PCR	MS	Disease risk	Two USP18 haplotypes were significantly associated with MS, TG and CG. Additional experiments revealed that CG carriers were characterized by lower USP18 gene expression levels in peripheral blood mononuclear cells and higher clinical disease activity. Finally, AA homozygosis for the intronic polymorphism rs2542109 was associated with the responder phenotype; however, USP18 expression levels induced by IFNb did not differ amongst MS patients carrying different rs2542109 genotypes	Ubiquitin specific peptidase 18 (USP18) is a deubiquitinating enzyme that functions as a negative regulator of the type I interferon (IFN) signalling pathway and is specifically induced by type I IFNs. In the present study, previous observations by our group were expanded suggesting an implication of USP18 in multiple sclerosis (MS) based on the finding of a deficient expression of the gene in peripheral blood mononuclear cells from MS patients compared with healthy controls	23700969	Details
TF	SNP	rs1049296	Real-time PCR	MS	Phenotypic risk	In the case of the rs1049269 codominant model of the TF polymorphism, the analysis showed that people with the CT genotype scored statistically significantly lower points in the EDSS scale at the diagnosis of the disease than those with the CC genotype .	TF plays a key role in the distribution and maintenance of iron homeostasis.It intermediates between the places of its storage, absorption, and use, delivering to all cells, including BVECs.The presence of polymorphisms in the genes of iron metabolism may modulate iron deposition in the body and thus affect the clinical course of the disease.	35682458	Details
USP18	SNP	rs9618216	real-time PCR	MS	Disease risk	Two USP18 haplotypes were significantly associated with MS, TG and CG. Additional experiments revealed that CG carriers were characterized by lower USP18 gene expression levels in peripheral blood mononuclear cells and higher clinical disease activity. Finally, AA homozygosis for the intronic polymorphism rs2542109 was associated with the responder phenotype; however, USP18 expression levels induced by IFNb did not differ amongst MS patients carrying different rs2542109 genotypes	Ubiquitin specific peptidase 18 (USP18) is a deubiquitinating enzyme that functions as a negative regulator of the type I interferon (IFN) signalling pathway and is specifically induced by type I IFNs. In the present study, previous observations by our group were expanded suggesting an implication of USP18 in multiple sclerosis (MS) based on the finding of a deficient expression of the gene in peripheral blood mononuclear cells from MS patients compared with healthy controls	23700969	Details
TF	SNP	rs3811647	Real-time PCR	MS	Phenotypic risk	It was observed that primary relapses were significantly more frequent in patients with AG and GG genotypes compared with the AA genotype in the recessive inheritance model for TF rs3811647.	TF plays a key role in the distribution and maintenance of iron homeostasis.It intermediates between the places of its storage, absorption, and use, delivering to all cells, including BVECs.The presence of polymorphisms in the genes of iron metabolism may modulate iron deposition in the body and thus affect the clinical course of the disease.	35682458	Details
TFR2	SNP	rs7385804	Real-time PCR	MS	Phenotypic risk	No statistically significant correlation was found between the TFR2 rs7385804 genotypes and the subjects with continuous variables in any of the analyzed inheritance models.	TFR2 has a lower affinity for TF than TFR1, it is mainly expressed in the mitochondria of dopaminergic neurons and, unlike TFR1, it is not controlled by intracellular iron levels because it lacks iron-sensitive elements.Research indicates the participation of TFR2 in the regulation of iron levels by influencing the indirect activation of hepcidin, the main regulator of iron levels in the body. TFR2 gene as a possible variant regulating iron levels in clinically healthy people.The presence of polymorphisms in the genes of iron metabolism may modulate iron deposition in the body and thus affect the clinical course of the disease.	35682458	Details
MIR146A	SNP	rs57095329	real-time PCR	MS	Disease risk	No significant differences were detected in the distribution of the two miR-146a polymorphisms between the patients and controls (P > 0.05).	N/A	25591770	Details
MIR146A	SNP	rs2910164	real-time PCR	MS	Disease risk	However, stratification by gender showed a statistically significant difference in the frequency of the genotype rs2910164 between MS patients and control females (P=0.009).	In this study, the observation that females have a higher MS prevalence than males may result from an interaction between the genotype and sex hormones during development.	25591770	Details
MIR146A	polymorphism	rs2910164 G>C	real-time PCR	MS	Disease risk	Further stratification analysis by subgroup revealed that the miR146a rs2910164 C allele conferred a higher risk of developing relapsing–remitting MS (RRMS (P=0.018).	It is likely that the rs2910164 G>C variation is linked with stronger inflammatory responses.	25591770	Details
CD40	SNP	rs1883832	Real-Time PCR	MS	Disease risk	The impact of CD40 rs1883832 on MS and CD risk points to a common signaling shared by these autoimmune conditions.	A functional polymorphism located at 21 from the start codon of the CD40 gene, rs1883832, was previously reported to disrupt a Kozak sequence essential for translation.	20634952	Details
RAC2	Allele	NA	Real-Time PCR	MS	Disease risk	Results suggest that a region covering the 3#untranslated region has been a target of multiallelic balancing selection (or diversifying selection), and three major RAC2 haplogroups occur in human populations. Haplotypes belonging to one of these clades are associated with increased susceptibility to multiple sclerosis (P 5 0.022) and earlier onset of disease symptoms (P 5 0.025).	The human RAC2 gene encodes a small GTP-binding protein with a pivotal role in immune activation and in the induction of peripheral immune tolerance through restimulation-induced cell death (RICD)	21680873	Details
PTPRC	SNP	polymorphism	real-time PCR	MS	Disease risk	These studies suggest that the regulation of CD45 splicing may be critical for the proper function of the immune system. Because of these data we examined the frequency of the C77G allele in African and Asian populations from countries with high or low prevalence of HIV infection. Here we report that the variant CD45 C77G allele is absent in African populations	Abstract The CD45 antigen is essential for normal antigen receptor-mediated signalling in lymphocytes, and different patterns of splicing of CD45 are associated with distinct functions in lymphocytes. Abnormal CD45 splicing has been recognized in humans, caused by a C77G transversion in the gene encoding CD45 (PTPRC)	11862398	Details
IL2RA	SNP	rs2104286	Real-time PCR	MS	Phenotypic risk	The annualized relapse rate in the rs2104286-TT genotype MS patients was significantly higher than that in the non-TT (CT+CC) genotype MS patients.The increased relapse rates in the rs2104286-TT genotype MS patients were only observed in females, and not in males.	N/A	24332945	Details
IL2RA	SNP	rs12722489	Real-time PCR	MS	Phenotypic risk	The MS patients with the rs12722489-CC genotype showed a significantly higher annualized relapse rate than the MS patients with the non-CC genotype.The increased relapse rates in the rs12722489-CC genotype MS patients were only observed in females, and not in males.	N/A	24332945	Details
IL2RA	SNP	rs7090512	Real-time PCR	MS	Phenotypic risk	No significant associations of any of the rs7090512 genotypes and allele frequencies with MS were observed.	N/A	24332945	Details
BIRC5	SNP	rs9904341	Real-time PCR	MS	phenotypics risk	It was observed that the C allele (OR = 1.38, 95% CI = 1.05–1.348, P = 0.022) and CC genotype (OR = 1.84,95% CI = 1.06–3.19; P = 0.029) in the rs9904341 polymorphism increased the disease risk.	The rs9904341 SNP was associated with increased mRNA and protein expressions of survi vin in cancers.	31438837	Details
CBLB	SNP	rs12487066	real-time PCR	MS	Treatment risk	The CBLB-rs12487066 gene polymorphisms showed a trend to association with change in the EDSS after 24 months of IFN treatment, but non-signifcant.	N/A	34169444	Details
GRIA3	SNP	rs12557782	real-time PCR	MS	Treatment risk	Women with the GG genotype of the rs12557782 polymorphism in the GRIA3 gene showed greater response to IFN-β.	N/A	34169444	Details
CTSS	SNP	rs1136774	real-time PCR	MS	Treatment risk	Patients with CC genotype in the rs1136774 polymorphism of the CTSS gene had greater response to IFN-β.	N/A	34169444	Details
OAS1	SNP	rs10774671	real-time PCR	MS	Treatment risk	The OAS1-rs10774671 gene polymorphism did not predict the variation of the individual response to IFN-β or change in the EDSS.	N/A	34169444	Details
TNFRSF10A	SNP	rs20576	real-time PCR	MS	Treatment risk	The TNFRSF10Ars20576 gene polymorphisms showed a trend to association with change in the EDSS after 24 months of IFN treatment,but non-signifcant.	N/A	34169444	Details
IFI16	CNV	rs1772408	real-time PCR	MS	Disease risk	After multiple test correction, none of the variants we analysed was significantly associated with the risk of developing MS.	N/A	24794504	Details
VDR	SNP	rs731236	Real-Time PCR	MS	Disease risk	This study suggests that the Taq-I and Bsm-I polymorphisms of the VDR gene are not associated with MS risk, BMI or BMD in the Greek population studied.	Polymorphisms of the vitamin D receptor (VDR) gene have been linked to both multiple sclerosis (MS) and osteoporosis. We examined the frequency of the Taq-I and Bsm-I polymorphisms of the vitamin D receptor (VDR) gene in 69 patients with MS and 81 age and sex-matched healthy individuals.	21545713	Details
IFI16	CNV	rs62621173	real-time PCR	MS	Disease risk	After multiple test correction, none of the variants we analysed was significantly associated with the risk of developing MS.	N/A	24794504	Details
VDR	SNP	rs1544410	Real-Time PCR	MS	Disease risk	This study suggests that the Taq-I and Bsm-I polymorphisms of the VDR gene are not associated with MS risk, BMI or BMD in the Greek population studied.	Polymorphisms of the vitamin D receptor (VDR) gene have been linked to both multiple sclerosis (MS) and osteoporosis. We examined the frequency of the Taq-I and Bsm-I polymorphisms of the vitamin D receptor (VDR) gene in 69 patients with MS and 81 age and sex-matched healthy individuals.	21545713	Details
IFI16	CNV	rs1772408	real-time PCR	MS	Disease risk	After multiple test correction, none of the variants we analysed was significantly associated with the risk of developing MS.	N/A	24794504	Details
IFI16	CNV	rs62621173	real-time PCR	MS	Disease risk	After multiple test correction, none of the variants we analysed was significantly associated with the risk of developing MS.	N/A	24794504	Details
CD6	SNP	rs17824933	Real-Time PCR	MS	Disease risk	We demonstrate significant association of rs17824933 in CD6 (PCMH= 0.004; OR= 1.14; 95% CI 1.04–1.24) and of rs1860545 in TNFRSF1A (PCMH= 0.001; OR= 1.15; 95% CI 1.06–1.25) with MS.	In addition, the soluble form of CD6 is capable of binding to various Gram-positive and -negative bacterial strains via recognition of pathogen-associated molecular patterns, and it downregulates serum levels of pro-inflammatory cytokines including IL-6, IL-1β and TNF-α upon challenge of mice with LPS.	20430450	Details
CXCL16	Allele	NA	Real-Time PCR	MS	Disease risk	The main finding of this study is gender-specific association of CXCL16 A181V polymorphism with susceptibility to MS in females.	CXC ligand 16 (CXCL16) is a multifunctional chemokine involved in cell adhesion and chemoattraction as well as in the scavenging of oxidized lipoproteins.Experimental data suggest the roles of CXCL16 in patho-genesis of multiple sclerosis (MS)	24854635	Details
IRF8	SNP	rs17445836	Real-Time PCR	MS	Disease risk	IRF8 could not be established beyond doubt as risk locus for MS due to the exclusion of the Bilbao and Madrid datasets.	N/A	20430450	Details
IFIH1	SNP	rs1990760	Real-Time PCR	MS	Disease risk	This study showed an association of rs1990760 polymorphism in the IFIH1 gene in the development of GD, LADA diabetes and MS within the Polish population.	The aim of the present study was to analyse a possible association of three autoimmune disabilities - Multiple sclerosis (MS), LADA diabetes and Graves’ disease (GD) with single nucleotide polymorphism (SNP; rs1990760) in the IF IH1 gene (also known as a melanoma differentiation-associated protein 5 - MDA5) within the Polish population	31733941	Details
TNFRSF1A	SNP	rs4149584	Real-Time PCR	MS	Disease risk	while the low-frequency coding non-synonymous SNP rs4149584 in TNFRSF1A displayed a trend for association (PCMH= 0.062; OR= 1.27; 95% CI 0.99–1.63).	N/A	20430450	Details
GPC5	SNP	rs10492503	Real-Time PCR	MS	Disease risk	The study suggests that genetic variants inGPC5, CD58 and IRF8 genes may be of clinical interest in MS as predictors of age of onset and response to therapy.	Multiple sclerosis (MS) is an autoimmune disease of the central nervous system with a neurodegen-erative compound. Heterogenetic background of autoimmunity pathway components has been suggested in the MS pathogenesis	30818222	Details
TNFRSF1A	SNP	rs1860545	Real-Time PCR	MS	Disease risk	We demonstrate significant association of rs17824933 in CD6 (PCMH= 0.004; OR= 1.14; 95% CI 1.04–1.24) and of rs1860545 in TNFRSF1A (PCMH= 0.001; OR= 1.15; 95% CI 1.06–1.25) with MS.	N/A	20430450	Details
CD58	Allele	NA	Real-Time PCR	MS	Disease risk	The study suggests that genetic variants inGPC5, CD58 and IRF8 genes may be of clinical interest in MS as predictors of age of onset and response to therapy.	Multiple sclerosis (MS) is an autoimmune disease of the central nervous system with a neurodegen-erative compound. Heterogenetic background of autoimmunity pathway components has been suggested in the MS pathogenesis	30818222	Details
IRF8	SNP	rs17445836	Real-Time PCR	MS	Disease risk	The study suggests that genetic variants inGPC5, CD58 and IRF8 genes may be of clinical interest in MS as predictors of age of onset and response to therapy.	Multiple sclerosis (MS) is an autoimmune disease of the central nervous system with a neurodegen-erative compound. Heterogenetic background of autoimmunity pathway components has been suggested in the MS pathogenesis	30818222	Details
ERVW-1	DNA copy number	N/A	real-time PCR	MS	Disease risk	HERV-W env transcription was found to be elevated in BD (Po10–4) and in SZ (P 0.012) as compared with HC, but with higher values in BD than in SZ group (Po0.01).	HERV-W envelope gene (env) is activated by environmental factors and encodes a protein displaying inflammation and neurotoxicity.	23212585	Details
IFIH1	SNP	rs1990760,	Real-Time PCR	MS	Disease risk	Therefore, genes included in this locus – IFIH1 interferon induced helicase,GCA grancalcin or the potassium channel KCNH7 – are potential candidates implicated in the pathogenesis of these autoimmune diseases, although strong linkage disequilibrium in the region hampered further localization of the etiologic gene.	A recent genome-wide scan of nonsynonymous SNPs and ulterior validation in case-control and family analyses evidenced a susceptibility locus for type 1 diabetes (T1D) on chromosome 2q24.3.	18285833	Details
KCNH7	SNP	rs2068330	Real-Time PCR	MS	Disease risk	Therefore, genes included in this locus – IFIH1 interferon induced helicase,GCA grancalcin or the potassium channel KCNH7 – are potential candidates implicated in the pathogenesis of these autoimmune diseases, although strong linkage disequilibrium in the region hampered further localization of the etiologic gene.	A recent genome-wide scan of nonsynonymous SNPs and ulterior validation in case-control and family analyses evidenced a susceptibility locus for type 1 diabetes (T1D) on chromosome 2q24.3.	18285833	Details
FOXP3	SNP	rs3761547	Real-Time PCR	MS	Disease risk	To our knowledge this is the first study which indicates gender-specific relation between rs3761547 FOXP3 gene polymorphism and multiple sclerosis.	The FOXP3 gene encodes a transcription factor and is predominantly expressed in the CD4+CD25+ regulatory T cells which plays a pivotal role in the maintenance of immune homeostasis.	30229436	Details
CD6	SNP	rs17824933	Real-time PCR	MS	Disease risk	In this study, the most significant association was seen with rs17824933.	N/A	27994359	Details
TMEM39A	SNP	rs1132200	Real-time PCR	MS	Disease risk	A modest association was also noted for TMEM39A rs1132200.	N/A	27994359	Details
LEP	SNP	rs7799039	Real-Time PCR	MS	Disease risk	Our study implicates a significant role of LEP and LEPR polymorphisms and also leptin levels in the risk of MS and its severity.	Leptin (LEP), leptin receptor (LEPR) and peroxisome proliferator-activated receptor gamma co- activator 1-alpha (PGC1A) are involved in the pathogenesis of multiple sclerosis (MS) by affecting the inflam-matory response and reactive oxygen species production.	27105071	Details
IL2RA	SNP	rs2104286	Real-time PCR	MS	Disease risk	A modest association was also noted for IL2RA rs2104286.	N/A	27994359	Details
LEPR	SNP	rs1137101	Real-Time PCR	MS	Disease risk	Our study implicates a significant role of LEP and LEPR polymorphisms and also leptin levels in the risk of MS and its severity.	Leptin (LEP), leptin receptor (LEPR) and peroxisome proliferator-activated receptor gamma co- activator 1-alpha (PGC1A) are involved in the pathogenesis of multiple sclerosis (MS) by affecting the inflam-matory response and reactive oxygen species production.	27105071	Details
PPARGC1A	SNP	rs8192678	Real-Time PCR	MS	Disease risk	Our study implicates a significant role of LEP and LEPR polymorphisms and also leptin levels in the risk of MS and its severity.	Leptin (LEP), leptin receptor (LEPR) and peroxisome proliferator-activated receptor gamma co- activator 1-alpha (PGC1A) are involved in the pathogenesis of multiple sclerosis (MS) by affecting the inflam-matory response and reactive oxygen species production.	27105071	Details
IL10	SNP	rs1800871, rs1800872, and rs1800896	real-time PCR	MS	Disease risk	The IL-10 rs1800871, rs1800872, and rs1800896 genotype and allele frequencies did not significantly differ between the MS and control groups.	Decreased IL-10 mRNA expression is observed at MS, which may be associated with promoter polymorphisms.IL-10 is an important cytokine regulator of the immune system, secreted mainly by macrophages and T lymphocytes.It is involved in the immune response to infectious and autoimmune diseases.IL-10 has an anti-inflammatory effect by reducing the production of immunoactive molecules (TNF-α, IFNγ, and IL-12) and inhibiting antigen-specific cytotoxic T cells.Since IL-10 may have an inflammatory function, it activates B cells and promotes autoantibody production.In the absence of IL-2, it inhibits T-cell apoptosis and promotes T-cell growth . It has been shown to increase the productivity of IL-10-producing cells.	35741685	Details
FOXP3	SNP	rs3761547, rs3761548	real-time PCR	MS	Disease risk	No statistically significant genotypic and allelic differences were found in the distribution of FOXP3 rs3761547 and rs3761548 in the MS patients, compared with controls.	Among these, the X-Linked Forkhead Box P3 (FoxP3) has a crucial role in Tregs development and stability, as shown by in vivo and in vitro studies.In particular, FOXP3-deficient Treg cells have been shown to reduce expression of Treg cell signature genes, such as TGF-β, IL-10, and CTLA4, which are critical for tolerance and immunosuppression, while gained the expression of cytokine genes, such as IFN-γ, TNF-α, and IL-17, which stimulate the immune response.Many polymorphisms in the gene codifying for Foxp3 have been associated with reduced levels of Foxp3 and impaired suppressive function of Treg cells, resulting in the development of autoimmune diseases.	33806248	Details
CD40	SNP	rs1883832C	Real-time PCR	MS	Disease risk	we examined the effect of three SNPs of CD40 (rs1883832C>T, rs11569343C>G, and rs752118C>T) and two SNPs of CD40L (rs3092923T>C and rs3092952A>G) on their mRNA expression. Our results showed that the rs1883832C>T SNP affects CD40 gene expression. Our analysis revealed that individuals possessing CT and TT genotypes (predisposing to MS) had decreased level of CD40 mRNA in comparison to those with CC	Abstract CD40-CD40L interactions mediate T-dependent B cell response and efficient T cell priming	25600834	Details
GATA3	SNP	rs3824662	real-time PCR	MS	Disease risk	No statistically significant genotypic and allelic differences were found in the distribution of GATA3 rs3824662 in the MS patients, compared with controls.	In vivo and in vitro studies showed that GATA3 expression has a fundamental role in maintaining high-levels of Foxp3 in Tregs.GATA3 has been reported to prevent excessive polarization toward Th17 and inflammatory cytokine production of Treg cells.Indeed, GATA-3-null Treg cells have been shown to fail to maintain peripheral homeostasis and suppressive function, shifting toward Th17 cell phenotypes and expressing reduced amounts of Foxp3.	33806248	Details
CD40	SNP	rs11569343C	Real-time PCR	MS	Disease risk	we examined the effect of three SNPs of CD40 (rs1883832C>T, rs11569343C>G, and rs752118C>T) and two SNPs of CD40L (rs3092923T>C and rs3092952A>G) on their mRNA expression. Our results showed that the rs1883832C>T SNP affects CD40 gene expression. Our analysis revealed that individuals possessing CT and TT genotypes (predisposing to MS) had decreased level of CD40 mRNA in comparison to those with CC	Abstract CD40-CD40L interactions mediate T-dependent B cell response and efficient T cell priming	25600834	Details
CD40	SNP	rs752118C	Real-time PCR	MS	Disease risk	we examined the effect of three SNPs of CD40 (rs1883832C>T, rs11569343C>G, and rs752118C>T) and two SNPs of CD40L (rs3092923T>C and rs3092952A>G) on their mRNA expression. Our results showed that the rs1883832C>T SNP affects CD40 gene expression. Our analysis revealed that individuals possessing CT and TT genotypes (predisposing to MS) had decreased level of CD40 mRNA in comparison to those with CC	Abstract CD40-CD40L interactions mediate T-dependent B cell response and efficient T cell priming	25600834	Details
CD40LG	SNP	rs3092923T	Real-time PCR	MS	Disease risk	we examined the effect of three SNPs of CD40 (rs1883832C>T, rs11569343C>G, and rs752118C>T) and two SNPs of CD40L (rs3092923T>C and rs3092952A>G) on their mRNA expression. Our results showed that the rs1883832C>T SNP affects CD40 gene expression. Our analysis revealed that individuals possessing CT and TT genotypes (predisposing to MS) had decreased level of CD40 mRNA in comparison to those with CC	Abstract CD40-CD40L interactions mediate T-dependent B cell response and efficient T cell priming	25600834	Details
CD40LG	SNP	rs3092952A	Real-time PCR	MS	Disease risk	we examined the effect of three SNPs of CD40 (rs1883832C>T, rs11569343C>G, and rs752118C>T) and two SNPs of CD40L (rs3092923T>C and rs3092952A>G) on their mRNA expression. Our results showed that the rs1883832C>T SNP affects CD40 gene expression. Our analysis revealed that individuals possessing CT and TT genotypes (predisposing to MS) had decreased level of CD40 mRNA in comparison to those with CC	Abstract CD40-CD40L interactions mediate T-dependent B cell response and efficient T cell priming	25600834	Details
VDR	SNP	rs731236	real-time PCR	MS	Disease risk	Significant differences emerged upon analyzing DRB1-rs731236 loci haplotypes in MS patients and HC.To summarize, the -DRB1-15-T haplotype was present in 9.9% of MS patients and in 4.4% of HC , whereas the -DRB1-15-C haplotype was detected in 7.4% of MS patients but only in 2.0% of HC.Results indicated a 7.88 fold increase of VDR mRNA in rs731236 TT compared to CC cells. Additionally, a 4.08-fold increase of VDR mRNA level was seen in CT compared to CC cells was observed.	The lack of variants in the VDRE sequence of the HLADRB115 allele led to the speculation that the augmented risk of MS seen in HLA-DRB115 carriers could be secondary to its transcription regulation through the VDR/(1,25(OH)2D) complex.	21664963	Details
MMP2	Allele	NA	Real-Time PCR	MS	Disease risk	The MMP-2 polymorphism led to a 5-year-earlier age of disease onset in MS patients with ON as a first symptom (p = 0.009).	N/A	26298319	Details
FCRL5	SNP	rs2012199	real-time PCR	MS	Disease risk	The CC genotype of rs2012199 has been identified only in individuals with MS.The CC and CT genotypes, as well as the C allele of rs2012199, were significantly more common in the MS subjects.We noted that decreased MS susceptibility was associated with the T allele rs2012199.	The activation of B-cells and the mediation of the specific recognition of antigens by leukocytes are promoted by a large family of Fc receptors.Human FCRL5 (Fc receptor-like protein 5) is a novel IgG receptor of the immunoglobulin superfamily (IgSF), and its expression is mainly restricted to B-cells.In subjects with high neurodegeneration, some changes in the peripheral blood mononuclear cells (PBMCs), including lower FCRL5 expression and higher peripheral blood B-cells activation status—characterized by a down-regulation of B-cell-specific genes—have been noted.	33889124	Details
FCRL5	SNP	rs6679793	real-time PCR	MS	Disease risk	Similar results were obtained for the genotypes and alleles of rs6679793.The OR of MS in subjects with the AG genotype was equal to 0.28 and 0.23 in subjects with the GG genotype.Allele A was significantly more common in MS subjects.The OR of MS was significantly lower in the G allele group.We noted that decreased MS susceptibility was associated with the G allele rs6679793.	The activation of B-cells and the mediation of the specific recognition of antigens by leukocytes are promoted by a large family of Fc receptors.Human FCRL5 (Fc receptor-like protein 5) is a novel IgG receptor of the immunoglobulin superfamily (IgSF), and its expression is mainly restricted to B-cells.In subjects with high neurodegeneration, some changes in the peripheral blood mononuclear cells (PBMCs), including lower FCRL5 expression and higher peripheral blood B-cells activation status—characterized by a down-regulation of B-cell-specific genes—have been noted.	33889124	Details
Il23a	Deletion	p19 -/- p19 +/- and p19 +/+	real-time PCR	EAE	Disease risk	Mice lacking IL-23 ( p19/) are resistant to EAE.	IL-23 may affect macrophage function directly.IL-23, unlike IL-12, acts more broadly as an end-stage effector cytokine through direct actions on macrophages.	12610626	Details
Ptgs2	Deletion	COX-2/	Real-time PCR	EAE	Treatment risk	Similar results were observed in COX-2/ mice, which developed less demyelination than COX-2+/+ mice after 5 weeks of cuprizone.In the cortex, only COX-2+/+ mice developed a significant demyelination.	Increased COX-2 expression in demyelinating lesions and increased PGs levels in the CSF of MS patients suggest that this pathway is involved in the disease, and studies in various animal models of demyelination support this concept.In the mouse model of Theiler’s encephalomyelitis virus (TMEV)-induced demyelination, COX-2 is expressed by mature oligodendrocytes undergoing apoptosis, suggesting that COX-2 plays a role in mediating oligodendrocytes apoptosis.	21699540	Details
VDR	SNP	TaqI(rs731236)	Real-Time PCR	MS	Disease risk	In conclusion, we found a significant association between MS and the FokI polymorphism in our region of Turkey.	N/A	29331875	Details
VDR	SNP	ApaI(rs7975232)	Real-Time PCR	MS	Disease risk	In conclusion, we found a significant association between MS and the FokI polymorphism in our region of Turkey.	N/A	29331875	Details
VDR	SNP	FokI(rs2228570)	Real-Time PCR	MS	Disease risk	In conclusion, we found a significant association between MS and the FokI polymorphism in our region of Turkey.	N/A	29331875	Details
FOXP3	genotype	rs3761548 CC	real-time PCR	MS	Disease risk	The frequencies of the AA genotype and A allele were significantly higher in the MS patients than in the healthy controls.	N/A	32988630	Details
FOXP3	genotype	rs3761548 CA	real-time PCR	MS	Disease risk	The frequencies of the AA genotype and A allele were significantly higher in the MS patients than in the healthy controls.	N/A	32988630	Details
FOXP3	genotype	rs3761548 AA	real-time PCR	MS	Disease risk	The frequencies of the AA genotype and A allele were significantly higher in the MS patients than in the healthy controls.	N/A	32988630	Details
FOXP3	allel	rs3761548 C	real-time PCR	MS	Disease risk	The frequencies of the AA genotype and A allele were significantly higher in the MS patients than in the healthy controls.	N/A	32988630	Details
FOXP3	allel	rs3761548 A	real-time PCR	MS	Disease risk	The frequencies of the AA genotype and A allele were significantly higher in the MS patients than in the healthy controls.	N/A	32988630	Details
FOXP3	genotype	rs3761548 CC	real-time PCR	MS	Disease risk	There was a significant association between FOXP3 rs3761548 variant and female MS patients.	N/A	32988630	Details
FOXP3	genotype	rs3761548 CA	real-time PCR	MS	Disease risk	There was a significant association between FOXP3 rs3761548 variant and female MS patients.	N/A	32988630	Details
FOXP3	genotype	rs3761548 AA	real-time PCR	MS	Disease risk	There was a significant association between FOXP3 rs3761548 variant and female MS patients.	N/A	32988630	Details
FOXP3	allel	rs3761548 C	real-time PCR	MS	Disease risk	There was a significant association between FOXP3 rs3761548 variant and female MS patients.	N/A	32988630	Details
FOXP3	allel	rs3761548 A	real-time PCR	MS	Disease risk	There was a significant association between FOXP3 rs3761548 variant and female MS patients.	N/A	32988630	Details
FOXP3	allel	rs3761548 C	real-time PCR	MS	Disease risk	There was a significant association between FOXP3 rs3761548 variant and female MS patients.	N/A	32988630	Details
FOXP3	allel	rs3761548 A	real-time PCR	MS	Disease risk	There was a significant association between FOXP3 rs3761548 variant and female MS patients.	N/A	32988630	Details
KIF5A	SNP	rs703842	real-time PCR	MS	Phenotypic risk	Multivariate analysis showed a significant effect of patient rs703842 genotype (AA vs AG) on CSF KIF5A levels, alongside disease subtype and a range of independent cohort variables.	Both hypo- and hyper- phosphorylation of NFs within axons are recognised as pathological hallmarks of MS and it is believed dysregulated axonal transport could be a catalyst for aberrant protein phosphorylation and accumulation.The majority of anterograde axonal transport is governed by kinesin superfamily motor proteins (KIFs). KIF5A is the main kinesin subtype involved in anterograde transport of phosphorylated NFs.	33484325	Details
KIF5A	SNP	rs12368653	real-time PCR	MS	Phenotypic risk	There was a significantly shorter MS duration in patients homozygous for rs12368653 risk SNP AA vs GG.	Both hypo- and hyper- phosphorylation of NFs within axons are recognised as pathological hallmarks of MS and it is believed dysregulated axonal transport could be a catalyst for aberrant protein phosphorylation and accumulation.The majority of anterograde axonal transport is governed by kinesin superfamily motor proteins (KIFs). KIF5A is the main kinesin subtype involved in anterograde transport of phosphorylated NFs.	33484325	Details
VDR	SNP	rs2228570	real-time PCR using TaqMan probes	MS	Disease risk	TT genotype for VDR FokI (rs2228570) polymorphism was associated with higher risk of MS (P = 0.0150; OR = 1.82; 95% CI = 1.12-2.94; TT vs. CT + CC).	Vitamin D metabolism	33044390	Details
VDR	SNP	rs7975232	real-time PCR using TaqMan probes	MS	N/A	We found no influence of the ApaI (rs7975232), BsmI (rs1544410), Cdx2 (rs11568820), FokI (rs2228570), and TaqI (rs731236) gene polymorphisms on the risk of developing MS in our patients.	Vitamin D metabolism	33044390	Details
VDR	SNP	rs1544410	real-time PCR using TaqMan probes	MS	N/A	We found no influence of the ApaI (rs7975232), BsmI (rs1544410), Cdx2 (rs11568820), FokI (rs2228570), and TaqI (rs731236) gene polymorphisms on the risk of developing MS in our patients.	Vitamin D metabolism	33044390	Details
VDR	SNP	rs11568820	real-time PCR using TaqMan probes	MS	N/A	We found no influence of the ApaI (rs7975232), BsmI (rs1544410), Cdx2 (rs11568820), FokI (rs2228570), and TaqI (rs731236) gene polymorphisms on the risk of developing MS in our patients.	Vitamin D metabolism	33044390	Details
VDR	SNP	rs2228570	real-time PCR using TaqMan probes	MS	N/A	We found no influence of the ApaI (rs7975232), BsmI (rs1544410), Cdx2 (rs11568820), FokI (rs2228570), and TaqI (rs731236) gene polymorphisms on the risk of developing MS in our patients.	Vitamin D metabolism	33044390	Details
VDR	SNP	rs731236	real-time PCR using TaqMan probes	MS	N/A	We found no influence of the ApaI (rs7975232), BsmI (rs1544410), Cdx2 (rs11568820), FokI (rs2228570), and TaqI (rs731236) gene polymorphisms on the risk of developing MS in our patients.	Vitamin D metabolism	33044390	Details
FAS	SNP	rs2234767	Real-time polymerase chain reaction	MS	Disease risk	The G/А genotype and the А-allele were associated with the increased risk of multiple sclerosis.	N/A	28617356	Details
VDR	SNP	rs10877013	Real-Time qPCR	MS	Disease risk	The MS-associated variant rs10877013 is a genetic determinant that affects the functioning of the vitamin D system linking environmental and genetic factors.	Vitamin D deficit is considered an important risk factor for many inflammatory and autoimmune diseases.	26466946	Details
IFNAR1	SNP	rs# 2243590,rs# 2252931,rs# 2243600	real-time TaqMan	MS	Disease risk	genetic variants in the IRF-1 and Stat1 genes of the IFN pathway are associated with MS and HCV infection	N/A	183388947	Details
IFNAR2	SNP	rs# 2300370,rs# 2248412,rs# 2834154,rs# 2154430,rs# 2236756,rs# 2284549,rs# 2284551,rs# 2834163,rs #2236757,rs #2236758	real-time TaqMan	MS	Disease risk	genetic variants in the IRF-1 and Stat1 genes of the IFN pathway are associated with MS and HCV infection	N/A	183388947	Details
STAT1	SNP	rs# 2066802,rs# 1547550	real-time TaqMan	MS	Disease risk	Compared to controls, Stat1 gene polymorphisms were significantly more frequent in MS patients	genetic variants in the IRF-1 and Stat1 genes of the IFN pathway are associated with MS and HCV infection	183388947	Details
STAT2	SNP	rs# 2066818,rs# 2066819,rs# 2020854,rs# 2066811	real-time TaqMan	MS	Disease risk	genetic variants in the IRF-1 and Stat1 genes of the IFN pathway are associated with MS and HCV infection	N/A	183388947	Details
IRF1	SNP	rs# 2070721	real-time TaqMan	MS	Disease risk	Also one IRF-1 gene SNP was associated with MS	genetic variants in the IRF-1 and Stat1 genes of the IFN pathway are associated with MS and HCV infection	183388947	Details
MIR196A2	SNP	rs1 1614913	realtime-PCR	MS	Disease risk	Variability of the MIR196A2 Gene as a Risk Factor in Primary-Progressive Multiple Sclerosis Development	The allele MIR196A2*C was useful in discriminating between two main courses of multiple sclerosis, one by one and in combination with alleles of the IFNAR2, IL7RA, IL6, PVT1, CD86, CCL5, and PSMB9 genes.	31099778	Details
C9orf72	expansion	N/A	Repeat Primed PCR	MS	Disease risk	No C9orf72 expansion reported showing no difference in the frequency of this mutation with respect to HCs .	C9orf72 is a gene encoding for two protein isoforms.Its function in cellular processes involves the regulation of membrane trafficking and gene expression. The expansion of C9orf72 gene induces the formation of repeat RNA aggregates that are shown to sequester proteins involved in RNA splicing, editing, nuclear export and nucleolar function.	26233805	Details
VDR	SNP	rs7975232	restriction fragment length polymorphisms (RFLPs).	MS	N/A	However, neither the genotype nor the allele frequency distribution was significantly different between the MS and control populations for the ApaI SNP.	N/A	25892553	Details
VDR	SNP	rs731236	restriction fragment length polymorphisms (RFLPs).	MS	Disease risk	Our results show a significant difference of the allelic frequency distribution between the case and control groups for TaqI SNP (P = 0.01), but genotype frequencies were not significantly different (P = 0.07 and 0.23).	N/A	25892553	Details
HLA-DRB1	allele	N/A	reverse dot-blot method	MS	Disease risk	A significant difference between patients and expected values was noted.The HLA-DRB1*15 allele was found more commonly in MS patients than in controls.A second HLA-DRB1 allele, HLA-DRB1*03, was found significantly more frequently in the patient group after this manoeuvre.The presence of HLA-DRB1*15 was estimated to give an approximately five-fold risk of MS.The risk in HLA-DRB1*15 homozygotes was not statistically different to the risk in HLA-DRB1*15 heterozygotes.	N/A	11374095	Details
HLA-DRB1	allele	N/A	reverse dot-blot method	MS	Treatment risk	HLA-DRB1*15 status was not significantly associated with outcome. When assessing the effect of HLA-DRB1*15 on outcome in the total patient group using logistic regression, including disease duration, gender and age at onset as covariates no significant relationships were noted.	N/A	11374095	Details
ERG	polymorphism	PvuII	RFLP	MS	Disease risk	The rate of PP and Pp genotype and the [P] allele frequency were significantly higher in MS patients than in controls, both in the total study population and in female subjects.	Biological actions of estrogen are mediated through intranuclear estrogen receptors, and estrogen receptors (ER) are expressed in cells involved in the immune response.	12098513	Details
ERG	polymorphism	Xba	RFLP	MS	Disease risk	The genotype and allele frequencies of Xba polymorphism were similar in MS patients and controls.	Biological actions of estrogen are mediated through intranuclear estrogen receptors, and estrogen receptors (ER) are expressed in cells involved in the immune response.	12098513	Details
MBP	DNA length polymorphism	RraI, EcoR	RFLP	MS	Disease risk	These data suggest that patients with MS differ from population-matched control subjects with respect to DNA polymorphism linked to the myelin basic protein gene but no pathogenic relationship between this polymorphism and MS can be presupposed.	Parallels between EAE and MS suggest that MBP polymorphism could result in enhanced MBP autoantigenicity, thereby contributing to autoimmune CNS demyelination .	1691612	Details
IGHM	haplotypes	N/A	RFLP	MS	Disease risk	No significant allelic or haplotypic association was observed.Linkage without a population association suggests that a gene encoded on 14q confers susceptibility to multiple sclerosis.	N/A	8568530	Details
DHX58	SNP	rs2074158	RFLP	MS	Disease risk	Evaluation of single nucleotide polymorphisms (SNPs) in the gene did not reveal significant single-SNP associations with MS risk.	Increased activation of RLR genes has been demonstrated in peripheral blood cells of MS patients.It was speculated that genetic alterations in the RIG-I-like receptor signaling pathway may lead to inadequate immune responses and increase the susceptibility for autoimmune disorders.	25288302	Details
SLC11A1	SNP	rs2276631	RFLP	MS	Disease risk	Only rs2276631 SNP was associated with MS	due to polymorphisms in immunomodulating the SLC11A1 gene	23492997	Details
SLC11A1	SNP	rs3731865	RFLP	MS	Disease risk	Only rs2276631 SNP was associated with MS	due to polymorphisms in immunomodulating the SLC11A1 gene	23492997	Details
SLC11A1	SNP	rs3731864	RFLP	MS	Disease risk	Only rs2276631 SNP was associated with MS	due to polymorphisms in immunomodulating the SLC11A1 gene	23492997	Details
SLC11A1	SNP	rs17221959	RFLP	MS	Disease risk	Only rs2276631 SNP was associated with MS	due to polymorphisms in immunomodulating the SLC11A1 gene	23492997	Details
SLC11A1	SNP	rs2695342	RFLP	MS	Disease risk	Only rs2276631 SNP was associated with MS	due to polymorphisms in immunomodulating the SLC11A1 gene	23492997	Details
SLC11A1	SNP	rs2279015	RFLP	MS	Disease risk	Only rs2276631 SNP was associated with MS	due to polymorphisms in immunomodulating the SLC11A1 gene	23492997	Details
SLC11A1	SNP	rs17235409	RFLP	MS	Disease risk	Only rs2276631 SNP was associated with MS	due to polymorphisms in immunomodulating the SLC11A1 gene	23492997	Details
SLC11A1	SNP	rs17235416	RFLP	MS	Disease risk	Only rs2276631 SNP was associated with MS	due to polymorphisms in immunomodulating the SLC11A1 gene	23492997	Details
PECAM1	allele	Amplicon length (bp):P1 (119),P2 (121),P3 (123),P4 (125),P5 (127),P6 (129),P7 (131)	RFLP	MS	Disease risk	After correction of the resulting P-values using the Bonferroni method, no statistical evidence for association with disease was left.	N/A	10900349	Details
MPO	allele	N/A	RFLP	MS	Disease risk	No differences in AF and PF between the Swedish case and control samples were observed.	N/A	10900349	Details
MPO	SNP	G/G, G/A and A/A	RFLP	MS	Disease risk	Genotyping of all Swedish subjects revealed no evidence for any effect of the MPO locus on MS development.	N/A	10900349	Details
PRKAR1A	allele	N/A	RFLP	MS	Disease risk	The resulting Swedish genotypes revealed no preponderance of any allele, neither in the case, nor in the control group.	N/A	10900349	Details
TRA	polymorphism	N/A	RFLP and a microsatellite repeat polymorphism	MS	Disease risk	The observed frequencies of haplotype sharing did not differ from expected rates and these results provide no evidence for linkage between the TCRa locus and susceptibility to MS.	Immune mechanisms are involved in the pathogenesis of MS. The areas of demyelination are infiltrated by lymphocytes and activated macrophages and various cytokines.Associations between MS and major histocompatibility complex (MHC) antigens are well established.Interactions occur between the MHC molecule, antigen and the heterodimeric T cell receptor (TCR) and this recognition process has stimulated interest in the role of TCR germline genes as additional candidates for susceptibility in a number of autoimmune diseases.	7931419	Details
HLA-DRB1	allele	DRBl*I501,DRBS*0I01,DQAl*OlO2,DQB1*0602	RFLP and PCR-SSP	MS	Disease risk	All Dw2-positive MS patients and control subjects carried the DRBl* 1501 allele.All Dw2-positive patients as well as the 30 Dw2-positive controls carried the DRBS *0101 allele.The Dw2 haplotype was found to include the DRBS*OlOl allele in all the sixteen Dw2 homozygous MS patients and six Dw2 homozygous healthy controls. We have found that the HLA-Dw2 haplotype in MS patients extends to the DRB5 locus. The haplotype associated with MS can thus be specified as DRBl*I501,DRBS*0I01,DQAl*OlO2,DQB1*0602.	N/A	8560455	Details
TAP1	dimorphisms	N/A	RFLP,PCR	MS	Disease risk	Previous studies have suggested that linkage disequilibrium may occur between TAP loci and some alleles of HLA-DR; in particular, linkage disequilibrium was observed between TAP2 and HLA-DR and -DQ, with evidence that a recombination hot spot may exist between TAP1 and TAP2.	N/A	8016841	Details
TAP2	dimorphisms	N/A	RFLP,PCR	MS	Disease risk	Previous studies have suggested that linkage disequilibrium may occur between TAP loci and some alleles of HLA-DR; in particular, linkage disequilibrium was observed between TAP2 and HLA-DR and -DQ, with evidence that a recombination hot spot may exist between TAP1 and TAP2.	N/A	8016841	Details
HLA-DRB1	allele-haplotype	N/A	RFLP,PCR	MS	Disease risk	We found a negative association between MS susceptibility and DR1-DQ5 haplotype.	The class II MHC proteins, the major restriction elements for cell-mediated immunity, have a pivotal role in development of the T-cell repertoire during ontogeny and subsequently in immune recognition. Hence, MHC genes are plausible candidate genes that could influence the outcome of an immune-mediated disease such as MS.	9748020	Details
HLA-DRB1	allele-haplotype	N/A	RFLP,PCR	MS	Phenotypic risk	We found a trend to a positive association of primary progressive MS with DR1-DQ5.	The class II MHC proteins, the major restriction elements for cell-mediated immunity, have a pivotal role in development of the T-cell repertoire during ontogeny and subsequently in immune recognition. Hence, MHC genes are plausible candidate genes that could influence the outcome of an immune-mediated disease such as MS.	9748020	Details
HLA-DRB2	allele-haplotype	N/A	RFLP,PCR	MS	Disease risk	We found a positive association between MS susceptibility and the DR15-DQ6 haplotypes.	The class II MHC proteins, the major restriction elements for cell-mediated immunity, have a pivotal role in development of the T-cell repertoire during ontogeny and subsequently in immune recognition. Hence, MHC genes are plausible candidate genes that could influence the outcome of an immune-mediated disease such as MS.	9748020	Details
HLA-DRB3	allele-haplotype	N/A	RFLP,PCR	MS	Phenotypic risk	We found a trend to a positive association association of "bout onset" MS with DR17-DQ2.	The class II MHC proteins, the major restriction elements for cell-mediated immunity, have a pivotal role in development of the T-cell repertoire during ontogeny and subsequently in immune recognition. Hence, MHC genes are plausible candidate genes that could influence the outcome of an immune-mediated disease such as MS.	9748020	Details
HLA-DRB4	allele-haplotype	N/A	RFLP,PCR	MS	Phenotypic risk	We found a trend to a positive association of primary progressive MS with DR4-DQ8 .	The class II MHC proteins, the major restriction elements for cell-mediated immunity, have a pivotal role in development of the T-cell repertoire during ontogeny and subsequently in immune recognition. Hence, MHC genes are plausible candidate genes that could influence the outcome of an immune-mediated disease such as MS.	9748020	Details
HLA-DRB6	allele-haplotype	N/A	RFLP,PCR	MS	Disease risk	We found a positive association between MS susceptibility and DR13-DQ7 haplotypes (both are DR6).	The class II MHC proteins, the major restriction elements for cell-mediated immunity, have a pivotal role in development of the T-cell repertoire during ontogeny and subsequently in immune recognition. Hence, MHC genes are plausible candidate genes that could influence the outcome of an immune-mediated disease such as MS.	9748020	Details
HLA-DQB1	allele-haplotype	N/A	RFLP,PCR	MS	Phenotypic risk	We found a trend to a positive association of primary progressive MS with DR4-DQ8 and DR1-DQ5 and an association of "bout onset" MS with DR17-DQ2.	The class II MHC proteins, the major restriction elements for cell-mediated immunity, have a pivotal role in development of the T-cell repertoire during ontogeny and subsequently in immune recognition. Hence, MHC genes are plausible candidate genes that could influence the outcome of an immune-mediated disease such as MS.	9748020	Details
HLA-DQB1	allele-haplotype	N/A	RFLP,PCR	MS	Disease risk	We found a positive association between MS susceptibility and the DR15-DQ6 and DR13-DQ7 haplotypes, and we found a negative association with the DR1-DQ5 haplotype.	The class II MHC proteins, the major restriction elements for cell-mediated immunity, have a pivotal role in development of the T-cell repertoire during ontogeny and subsequently in immune recognition. Hence, MHC genes are plausible candidate genes that could influence the outcome of an immune-mediated disease such as MS.	9748020	Details
HLA-DRB1	allele	N/A	RFLP,PCR-SSP	MS	Disease risk	The frequency of the DRB1*1503 haplotype had increased significantly among the DR2-positive MS patients compared with the DR2-positive control group. The DRB1*15021 haplotype was negatively associated with MS.	N/A	9777330	Details
HLA-DQB1	allele	N/A	RFLP,PCR-SSP	MS	Disease risk	The frequency of the DQB1*0602 haplotype had increased significantly among the DR2-positive MS patients compared with the DR2-positive control group.The DQB1*0601 haplotype was negatively associated with MS.	N/A	9777330	Details
HLA-DQA1	allele	N/A	RFLP,PCR-SSP	MS	Disease risk	The frequency of the DQA1*0102 haplotype had increased significantly among the DR2-positive MS patients compared with the DR2-positive control group.The DQA1*0103 haplotype was negatively associated with MS.	N/A	9777330	Details
HLA-DPB1	polymorphism	N/A	RFLP,Southern Blot	MS	N/A	We detected no polymorphisms of DR beta, DQ alpha, or DQ beta genes among the DR2+ MS patients which distinguished them from normals.	N/A	2568496	Details
IL2	polymorphisms	-475 AA	RFLP-PCR	MS	Disease risk	Our results showed that in this population of Iraqi patients, the AT genotype / A allele of -475 IL-2 promoter gene SNP may include attributed factors for MS predisposition.	N/A	35765522	Details
IL2	polymorphisms	-475 AT	RFLP-PCR	MS	Disease risk	Our results showed that in this population of Iraqi patients, the AT genotype / A allele of -475 IL-2 promoter gene SNP may include attributed factors for MS predisposition.	N/A	35765522	Details
IL2	polymorphisms	-475 TT	RFLP-PCR	MS	Disease risk	Our results showed that in this population of Iraqi patients, the AT genotype / A allele of -475 IL-2 promoter gene SNP may include attributed factors for MS predisposition.	N/A	35765522	Details
IL2	polymorphisms	-475 A	RFLP-PCR	MS	Disease risk	Our results showed that in this population of Iraqi patients, the AT genotype / A allele of -475 IL-2 promoter gene SNP may include attributed factors for MS predisposition.	N/A	35765522	Details
IL2	polymorphisms	-475 T	RFLP-PCR	MS	Disease risk	Our results showed that in this population of Iraqi patients, the AT genotype / A allele of -475 IL-2 promoter gene SNP may include attributed factors for MS predisposition.	N/A	35765522	Details
HAVCR2	SNP	rs1036199	RFLP-PCR	MS	Disease risk	Our findings suggest that +4259 A > C polymorphism in TIM-3 gene may be one of the important genetic factors associated with the MS susceptibility among Iranian populations.	Multiple sclerosis (MS) is an inflammatory disease of the central nervous system (CNS) which in-itiated and mediated by autoreactive T helper1 cells directed against myelin antigens.	29141799	Details
HAVCR1	SNP	rs7702919	RFLP-PCR	MS	Disease risk	We found that the polymorphism +4259 A > C in exon 3 of the TIM-3 gene is associated with sus-ceptibility to the MS but the other polymorphism,in the promoter region of TIM-1 is not (p= 0.064).	Multiple sclerosis (MS) is an inflammatory disease of the central nervous system (CNS) which in-itiated and mediated by autoreactive T helper1 cells directed against myelin antigens.	29141799	Details
HAVCR2	SNP	rs10515746	RFLP-PCR	MS	Disease risk	In this case-control study, analysis of the alleles and genotypes revealed a significant higher frequency of C/C and lower frequency of A/C genotypes for -574 locus of TIM-3 gene in MS patients. Allele C of -574C/C was also more frequent in MS patients.	TIM-3 is a negative regulator of immune responses that specially expressed on activated Th1 cells, CD8+ T cells and at a lower level on Th17 cells but not on Th2 cells.Dysregulated expression of TIM-3 on T-cells resulted in enhanced T-cell proliferation and IFN-γ secretion following T-cell stimulation. TIM-3 interacts with its ligand (Galectin-9) to regulate T cells responses.Evidence indicates a dysfunction of TIM-3 immunoregulation in MS disease.	27398337	Details
HAVCR2	SNP	rs10053538	RFLP-PCR	MS	Disease risk	We also found that C/C genotype for locus of -1516 increased in MS patients, while A/C genotype decreased.-1516 C>A SNP was also more frequent in MS patients.	TIM-3 is a negative regulator of immune responses that specially expressed on activated Th1 cells, CD8+ T cells and at a lower level on Th17 cells but not on Th2 cells.Dysregulated expression of TIM-3 on T-cells resulted in enhanced T-cell proliferation and IFN-γ secretion following T-cell stimulation. TIM-3 interacts with its ligand (Galectin-9) to regulate T cells responses.Evidence indicates a dysfunction of TIM-3 immunoregulation in MS disease.	27398337	Details
IL21	SNP	rs2221903	RFLP-PCR	MS	Disease risk	Our results showed that the IL-21 rs2221903 SNP is not polymorphic in our population.	Along with TH1 cells, IL-17-producing CD4+ T cells (TH-17) play important roles in the pathogenesis of experimental autoimmune encephalomyelitis (EAE), an animal model of MS which are also found at high frequency in active MS lesions.IL-21, IL-6 and IL-22 are the other products of TH17 cells which also may involve in the disease process.IL-21 is a potent immunomodulatory cytokine with pleiotropic effects on both innate and adaptive immune responses.This cytokine enhances proliferation of lymphoid cells, increases cytotoxicity of CD8+ T cells and natural killer cells, and differentiation of B cells into plasma cells.IL-21 is found to synergize with TGF-β to induce RORγt and IL-17 in naive T cells and thereby augments the differentiation of Th17 cell, which also secrete IL-21, indicating that IL-21 auto-regulates its own production.	26155434	Details
IL21	SNP	rs2055979	RFLP-PCR	MS	Disease risk	The allelic and genotypic frequencies of the IL-21 rs2055979 did not differ significantly between the MS patients and controls.	Along with TH1 cells, IL-17-producing CD4+ T cells (TH-17) play important roles in the pathogenesis of experimental autoimmune encephalomyelitis (EAE), an animal model of MS which are also found at high frequency in active MS lesions.IL-21, IL-6 and IL-22 are the other products of TH17 cells which also may involve in the disease process.IL-21 is a potent immunomodulatory cytokine with pleiotropic effects on both innate and adaptive immune responses.This cytokine enhances proliferation of lymphoid cells, increases cytotoxicity of CD8+ T cells and natural killer cells, and differentiation of B cells into plasma cells.IL-21 is found to synergize with TGF-β to induce RORγt and IL-17 in naive T cells and thereby augments the differentiation of Th17 cell, which also secrete IL-21, indicating that IL-21 auto-regulates its own production.	26155434	Details
IL21	SNP	rs2055979	RFLP-PCR	MS	Phenotypic risk	Our results showed that IL-21 rs2055979 (G/T) T allele positive (TT+GT) MS patients had lower disease progression compared to rs2055979 T allele negative (GG) patients.	Along with TH1 cells, IL-17-producing CD4+ T cells (TH-17) play important roles in the pathogenesis of experimental autoimmune encephalomyelitis (EAE), an animal model of MS which are also found at high frequency in active MS lesions.IL-21, IL-6 and IL-22 are the other products of TH17 cells which also may involve in the disease process.IL-21 is a potent immunomodulatory cytokine with pleiotropic effects on both innate and adaptive immune responses.This cytokine enhances proliferation of lymphoid cells, increases cytotoxicity of CD8+ T cells and natural killer cells, and differentiation of B cells into plasma cells.IL-21 is found to synergize with TGF-β to induce RORγt and IL-17 in naive T cells and thereby augments the differentiation of Th17 cell, which also secrete IL-21, indicating that IL-21 auto-regulates its own production.	26155434	Details
A2M	Deletion	Exon 18Del	RFLP-PCR	MS	Disease risk	We did not observe significant differences for the genotype and the allele frequency of the Exon 18Del.	Several biological functions have been described for A2M.The structure of the protein suggests a function as protein inhibitor.Furthermore, A2M binds to cytokines and seems to inactivate at least some of themThe protein also enhances antigen-driven immune responses by capturing antigen for presentation.	11498265	Details
A2M	polymorphism	Val 1000 Iso	RFLP-PCR	MS	Disease risk	We did not observe significant differences for the genotype and the allele frequency of the polymorphisms Val 1000 Iso.	Several biological functions have been described for A2M.The structure of the protein suggests a function as protein inhibitor.Furthermore, A2M binds to cytokines and seems to inactivate at least some of themThe protein also enhances antigen-driven immune responses by capturing antigen for presentation.	11498265	Details
LRP6	polymorphism	A216V	RFLP-PCR	MS	Disease risk	The homozygous expression of the A216V polymorphism was not observed in any of the MS patients or controls.	LRP serves as a receptor for A2M and apolipoprotein E. Its distribution in the brain is consistent with a potential function in the regulation of proteinase activity, cytokine activity, and cholesterol metabolism.	11498265	Details
TRBV20OR9-2	polymorphism	N/A	RFLPs	MS	Disease risk	A total of 267 families with two or more siblings with multiple sclerosis (MS) were genotyped with 14 restriction fragment length polymorphisms at the TCR beta locus.A nonparametric linkage analysis of the data showed no evidence for linkage to this locus . No significant allelic or haplotype transmissions were observed in the total sample of 565 patients.	An initial positive association of a TCR a rearrangement in multiple sclerosis brains (MS).	15175643	Details
COX2	polymorphisms in this COX-2 region	765G>C and 62C>G	RG-PCR	MS	N/A	polymorphisms in this COX-2 region are unlikely to be involved in MS susceptibility.	N/A	17373929	Details
TAGAP	SNP	rs1738074,rs3127214	RT and real-time PCR	Curdlan and α-mannan stimulated	Disease risk	We found that PBMCs from individuals carries the TAGAP rs1738074 C/C genotype had the significant higher TAGAP mRNA expression levels compared with that from rs1738074 T/C and T/T carriers, whereas PBMCs of rs3127214 T/T carriers had significantly lower TAGAP mRNA levels compared with that of rs3127214 C/T and C/C carriers .Furthermore, Th17 cell abundance was positively correlated with the TAGAP mRNA levels in PBMCs from both of two genotypes.The lower Th17 abundance in the PBMCs of rs3127214 polymorphism carrier could very well explain its susceptibility to candidemia, as Th17 cells were known to play the most critical role in host defense against fungi, such as C. albicans. PBMC-induced proinflammatory gene expression in response to different stimuli was positively correlated with TAGAP mRNA level .	Th17 cells were known to play the most critical role in host defense against fungi, such as C. albicans.	32312989	Details
Tagap	Deletion	N/A	RT and real-time PCR,flow cytometry analysis, immunoblot analysis,H&E staining and LFB staining	EAE	Phenotypic risk	TAGAP-deficient mice showed a delay in the onset of neurological impairment and much lower disease severity.Perivascular leukocyte infiltration and demyelination were much more prominent in the spinal cords of heterozygous control mice compared with TAGAP-deficient mice.There was a marked decrease in the expression levels of ‘signature’ IL-17-responsive genes, such as CXCL1, CXCL2, IL-6, and IL-1β, in the spinal cords of TAGAP-deficient mice compared with heterozygous control mice. There was a great degree of mononuclear cell infiltration in the brain white matter and spinal cords of heterozygous control mice than in TAGAP-deficient mice .The Th17 and Th1 cells in the peripheral blood and brain were also comparable between Rag2-deficient mice transferred with wild-type or TAGAP-deficient CD4+ T cells.	N/A	32312989	Details
HLA-DPB1	Allele	NA	RT-PCR	MS	Disease risk	There was no statistically significant difference of the distributions of HLA-DPB1*0501/HLA-DPB1*0501, HLA-DPB1*0501/X and X/X genotypes and the frequencies of allele of HLA-DPB1*0501 among NMOSD, MS patients and healthy controls (P=0.96 and 0.71, respectively).	To investigate the effect of HLA-DP gene expression on the susceptibility and disease status of neuromyelitis optica spectrum disorders (NMOSD).	31826574	Details
CYP7A1	SNP	rs3808607	RT-PCR	MS	Disease risk	CYP7A1 rs3808607 and CYP46A1 rs754203 variations are not likely to confer an independent risk for MS development in the Turkish population.	Patients with multiple sclerosis (MS) have significantly lower vitamin D levels. Cholesterol is known to be the precursor for vitamin D synthesis, and cholesterol removal is regulated by cholesterol 7α-hydroxylase (CYP7A1) in the liver and cholesterol 24S-hydroxylase (CYP46A1) in the brain. In this study, single nucleotide polymorphisms (SNPs) within the genes CYP7A1 (rs3808607) and CYP46A1 (rs754203) were investigated for their effects on serum lipid profiles, vitamin D levels, and the risk of developing MS.	34546511	Details
CYP46A1	SNP	rs754203	RT-PCR	MS	Disease risk	CYP7A1 rs3808607 and CYP46A1 rs754203 variations are not likely to confer an independent risk for MS development in the Turkish population.	Patients with multiple sclerosis (MS) have significantly lower vitamin D levels. Cholesterol is known to be the precursor for vitamin D synthesis, and cholesterol removal is regulated by cholesterol 7α-hydroxylase (CYP7A1) in the liver and cholesterol 24S-hydroxylase (CYP46A1) in the brain. In this study, single nucleotide polymorphisms (SNPs) within the genes CYP7A1 (rs3808607) and CYP46A1 (rs754203) were investigated for their effects on serum lipid profiles, vitamin D levels, and the risk of developing MS.	34546511	Details
MEFV	gene variants	N/A	RT-PCR	MS	Treatment risk	carrying rare variants in MEFV was associated with the development of severe systemic side-effects upon IFN-å°¾ treatment.	N/A	23325590	Details
Tcrb	polymorphisms	Vb16	RT-PCR	EAE	Disease risk	Vb16 may recognize this terminal residue.	N/A	10358147	Details
TNF	gene polymorphisms	一308G／A	RT-PCR	MS	Disease risk	The TNF-ot level in soFIIIII is associated with active MS，but not in the CSF．The gene o p lymorphisms ofTNF-o．一308G／A is not associated with MS in Han nationality of southern China	gene polymorphisms	17160953	Details
IL1B	SNP	rs16944	RT-PCR	MS	Disease risk	We found that the expression level of IL-1B in MS patients increased 3.336 times more than controls in PBMCs but the rs16944 SNP in the promoter region of IL-1B did not affect the expression level of this gene and there was not association of this SNP with MS in the examined population	N/A	24867167	Details
ICAM1	Allele	NA	RT-PCR	MS	Disease risk	The results indicate increased frequency of ICAM-1 exon 6 allele T in MS patients, which may contribute to the MS genetics background.	Intracellular adhesion molecule-1 (ICAM-1) plays an important role in the cascade of adhesion events in the homing of inflammatory cells to the central nervous system (CNS) in experimental autoimmune encephalomyelitis (EAE) and in multiple sclerosis (MS).	9667594	Details
Eae23	allele	N/A	RT-PCR	EAE	N/A	There were no significant differences between the strains in either the shared region of ZEB1 or its downstream target IL2. However, mRNA expression of the splice variant Zfhep2 was higher in DA compared to PVG.1AV1mwhile there was no significant difference in Zfhep1.	N/A	20856809	Details
Eae23	allele	N/A	RT-PCR	EAE	N/A	No significant differences between the strains were seen in ZEB1, Zfhep1 or IL2,mRNA expression of the splice variant Zfhep2 was higher in DA and a trend of lower secreted IL-2 in DA were observed.	N/A	20856809	Details
Eae23	allele	N/A	RT-PCR	EAE	N/A	The shared region of ZEB1, Zfhep2 and IL2 were significantly up-regulated in DA compared to DA.PVG-Eae23, while Zfhep1 was significantly down-regulated in DA compared to DA.PVG-Eae23.	N/A	20856809	Details
GAPVD1	SNP	rs2291858	RT-PCR	MS	Disease risk	The results show that the GAPVD1 expression level and rs2291858 genotype probably affect the response to IFN-β in patients with MS.	affect the response to IFN- β in patients with MS.	33548618	Details
NLRP3	SNP	rs35829419	RT-PCR	MS	Disease risk	These results point to a role of the NLRP3 inflammasome and its related cytokine IL1B in the response to interferon beta in patients with relapsing-remitting multiple sclerosis.	A trend for association was observed between rs35829419 and interferon beta response	25586466	Details
CD24	SNP	NA	RT-PCR	MS	Disease risk	We found that the CD24v/v renders a >2-fold increase in the relative risk of MS in the general population	. Thus, CD24 polymorphism is a genetic modifier for susceptibility and progression of MS in the central Ohio cohort that we studied, perhaps by affecting the efficiency of CD24 expression on the cell surface	14657362	Details
INPP4B	SNP	rs13102150	RT-PCR	MS	Disease risk	An association of an INPP4B polymorphism (rs13102150) with MS was observed in German and Spanish MS cohorts (3676 controls and 911 cases)	An association of an INPP4B polymorphism (rs13102150) with MS was observed in German and Spanish MS cohorts (3676 controls and 911 cases)	25129256	Details
HOTAIR	SNP	rs920778	RT-PCR	MS	Disease risk	influenced the expression of HOTAIR	the VD pathway	29030863	Details
CDKN2B-AS1	SNP	rs10757278	RT-PCR	MS	Disease risk	disrupts a binding site for STAT1 influenced the expression of ANRIL	the VD pathway	29030863	Details
IGH	rearrangement	N/A	RT-PCR	MS	Disease risk	Significant rearrangement diversity and deviation from the normal Ig heavy(H) chain repertoire was observed.	N/A	10528220	Details
CDKN2B-AS1	SNP	rs1333045	RT-PCR	MS	Disease risk	functionally affect the activity of the 9p21	the VD pathway	29030863	Details
CETP	SNP	rs5882	RT-PCR	ON	Disease risk	We revealed that the genotypes of CETPrs708272 G/A, IL6rs1800795 G/G, and each allele C at VEGFArs833068 were associated with ON. CETPrs708272 G/G genotype was associated with decreased by 62% odds of ON with MS development under the recessive (OR = 0.379;95% CI:0.155–0.929; p = .034) model	It is thought that CETP, SIRT1, FGFR2, STAT3, VEGFA and IL6 genes play a key role in this autoimmune inflammatory disease	31199170	Details
CETP	SNP	rs708272	RT-PCR	ON	Disease risk	We revealed that the genotypes of CETPrs708272 G/A, IL6rs1800795 G/G, and each allele C at VEGFArs833068 were associated with ON. CETPrs708272 G/G genotype was associated with decreased by 62% odds of ON with MS development under the recessive (OR = 0.379;95% CI:0.155–0.929; p = .034) model	It is thought that CETP, SIRT1, FGFR2, STAT3, VEGFA and IL6 genes play a key role in this autoimmune inflammatory disease	31199170	Details
SIRT1	SNP	rs12778366	RT-PCR	ON	Disease risk	We revealed that the genotypes of CETPrs708272 G/A, IL6rs1800795 G/G, and each allele C at VEGFArs833068 were associated with ON. CETPrs708272 G/G genotype was associated with decreased by 62% odds of ON with MS development under the recessive (OR = 0.379;95% CI:0.155–0.929; p = .034) model	It is thought that CETP, SIRT1, FGFR2, STAT3, VEGFA and IL6 genes play a key role in this autoimmune inflammatory disease	31199170	Details
FGFR2	SNP	rs2981582	RT-PCR	ON	Disease risk	We revealed that the genotypes of CETPrs708272 G/A, IL6rs1800795 G/G, and each allele C at VEGFArs833068 were associated with ON. CETPrs708272 G/G genotype was associated with decreased by 62% odds of ON with MS development under the recessive (OR = 0.379;95% CI:0.155–0.929; p = .034) model	It is thought that CETP, SIRT1, FGFR2, STAT3, VEGFA and IL6 genes play a key role in this autoimmune inflammatory disease	31199170	Details
STAT3	SNP	rs744166	RT-PCR	ON	Disease risk	We revealed that the genotypes of CETPrs708272 G/A, IL6rs1800795 G/G, and each allele C at VEGFArs833068 were associated with ON. CETPrs708272 G/G genotype was associated with decreased by 62% odds of ON with MS development under the recessive (OR = 0.379;95% CI:0.155–0.929; p = .034) model	It is thought that CETP, SIRT1, FGFR2, STAT3, VEGFA and IL6 genes play a key role in this autoimmune inflammatory disease	31199170	Details
VEGFA	SNP	rs833068	RT-PCR	ON	Disease risk	We revealed that the genotypes of CETPrs708272 G/A, IL6rs1800795 G/G, and each allele C at VEGFArs833068 were associated with ON. CETPrs708272 G/G genotype was associated with decreased by 62% odds of ON with MS development under the recessive (OR = 0.379;95% CI:0.155–0.929; p = .034) model	It is thought that CETP, SIRT1, FGFR2, STAT3, VEGFA and IL6 genes play a key role in this autoimmune inflammatory disease	31199170	Details
IL6	SNP	rs1800795	RT-PCR	ON	Disease risk	We revealed that the genotypes of CETPrs708272 G/A, IL6rs1800795 G/G, and each allele C at VEGFArs833068 were associated with ON. CETPrs708272 G/G genotype was associated with decreased by 62% odds of ON with MS development under the recessive (OR = 0.379;95% CI:0.155–0.929; p = .034) model	It is thought that CETP, SIRT1, FGFR2, STAT3, VEGFA and IL6 genes play a key role in this autoimmune inflammatory disease	31199170	Details
MANBA	SNP	rs7665090	RT-PCR	MS	Disease risk	Our work provides new evidence highlighting the impact of the MS-risk variant, rs7665090, and the role of MANBA in the immunopathology of MS.	Significantly decreased enzymatic activity and lysosomal function and significantly lower lymphocyte and metabolic activations in response to stimulus were detected in MS carriers of the GG genotype compared to controls with the same genotype, while the rs7665090*AA genotype led to similar effects both in patients and controls.	35897697	Details
TNFRSF1A	SNP	rs1800693	RT-PCR	MS	Disease risk	no association with disease severity was observed for rs1800693	N/A	23624563	Details
TNFRSF1A	SNP	rs4149584	RT-PCR	MS	Disease risk	For rs4149584, R92Q carriers were younger at disease onset and progressed slower compared to noncarriers	N/A	23624563	Details
ID1	N/A	N/A	RT-PCR	MS	Disease risk	Statistically, the difference in the incidence of 14 of 31 MS patients compared with 2 of 19 non-MS subjects was significant.	N/A	9484364	Details
Ciita	allele	Vra4	RT-PCR	EAE	Disease risk	PVGav1-Vra4 rats displayed a lower disease incidence and milder disease course compared with DA, whereas both PVGav1 and PVGav1. DA-Vra4 rats were completely protected.	Naturally occurring allelic differences in Mhc2ta have profound effects on the quantity of MHC II expression in the CNS and on immune cells and that this genetic variability also modulates susceptibility to autoimmune neuroinflammation.	18292553	Details
ANKRD55	SNP	rs6859219	RT-PCR and quantitative PCR	MS	Disease risk	we found that the risk (C) allele of rs6859219 is associated with higher expression of ANKRD55 mRNA in PBMCS and CD4+ T cells	the high level of ANKRD55 increases susceptibility to pathologic inflammation	27183579	Details
IL22RA2	SNP	rs276474	RT-PCR and quantitative PCR	MS	Disease risk	The association of IL-22RA2 withbothEAE andMS strengthens its potential role in disease progression.	g macrophage effector mechanisms	21041731	Details
TNFAIP3	SNP	rs10499194	RT-PCR、TaqMan PCR	MS	Disease risk	We found significant association of rs10499194, located in the intergenic region upstream of TNFAIP3, with MS	evidence is accumulating that polymorphisms in both TNFAIP3 and TNFRSF1A genes play a role in MS pathogenesis	25684197	Details
TNFAIP3	SNP	rs6920220	RT-PCR、TaqMan PCR	MS	Disease risk	while rs69202220 and rs5029939 were less stronglu associated	evidence is accumulating that polymorphisms in both TNFAIP3 and TNFRSF1A genes play a role in MS pathogenesis	25684197	Details
TNFAIP3	SNP	rs5029939	RT-PCR、TaqMan PCR	MS	Disease risk	while rs69202220 and rs5029939 were less stronglu associated	evidence is accumulating that polymorphisms in both TNFAIP3 and TNFRSF1A genes play a role in MS pathogenesis	25684197	Details
TNFAIP3	SNP	rs6922466	RT-PCR、TaqMan PCR	MS	Disease risk	and rs6922466 did not show association with MS	evidence is accumulating that polymorphisms in both TNFAIP3 and TNFRSF1A genes play a role in MS pathogenesis	25684197	Details
TNFRSF1A	SNP	rs1800693	RT-PCR、TaqMan PCR	MS	Disease risk	the intronic SNP rs1800693 in TNFRSF1A showed moderate association with MS	evidence is accumulating that polymorphisms in both TNFAIP3 and TNFRSF1A genes play a role in MS pathogenesis	25684197	Details
TNFRSF1A	SNP	rs4149584	RT-PCR、TaqMan PCR	MS	Disease risk	while rs4149584 and R92Q did not show association with MS	evidence is accumulating that polymorphisms in both TNFAIP3 and TNFRSF1A genes play a role in MS pathogenesis	25684197	Details
TNFRSF1A	SNP	rs4149577	RT-PCR、TaqMan PCR	MS	Disease risk	the intronic SNP rs1800693 in TNFRSF1A showed moderate association with MS	evidence is accumulating that polymorphisms in both TNFAIP3 and TNFRSF1A genes play a role in MS pathogenesis	25684197	Details
TNFSF10	SNP	rs6763816	RT-qPCR	MS	Disease risk	These findings show a role for TRAILR-1 gene variations in the clinical outcome of IFN beta therapy that might have relevance as a biomarker to predict the response to IFN beta in MS.	death signal	23658636	Details
TNFSF10	SNP	rs11545817	RT-qPCR	MS	Disease risk	These findings show a role for TRAILR-2 gene variations in the clinical outcome of IFN beta therapy that might have relevance as a biomarker to predict the response to IFN beta in MS.	death signal	23658636	Details
TNFSF10	SNP	rs1047275	RT-qPCR	MS	Disease risk	These findings show a role for TRAILR-3 gene variations in the clinical outcome of IFN beta therapy that might have relevance as a biomarker to predict the response to IFN beta in MS.	death signal	23658636	Details
TNFSF10	SNP	rs16845759	RT-qPCR	MS	Disease risk	These findings show a role for TRAILR-4 gene variations in the clinical outcome of IFN beta therapy that might have relevance as a biomarker to predict the response to IFN beta in MS.	death signal	23658636	Details
TNFSF10	SNP	rs7011559	RT-qPCR	MS	Disease risk	These findings show a role for TRAILR-5 gene variations in the clinical outcome of IFN beta therapy that might have relevance as a biomarker to predict the response to IFN beta in MS.	death signal	23658636	Details
TNFSF10	SNP	rs4491934	RT-qPCR	MS	Disease risk	These findings show a role for TRAILR-6 gene variations in the clinical outcome of IFN beta therapy that might have relevance as a biomarker to predict the response to IFN beta in MS.	death signal	23658636	Details
TNFSF10	SNP	rs1131579	RT-qPCR	MS	Disease risk	These findings show a role for TRAILR-7 gene variations in the clinical outcome of IFN beta therapy that might have relevance as a biomarker to predict the response to IFN beta in MS.	death signal	23658636	Details
PTPRC	SNP	exon 4 (C→G nucleotide transition in position 77)	RT–PCR and PCR,flow cytometry	MS	Disease risk	The altered CD45 expression phenotype is associated with MS,in almost all cases, the altered expression is caused by a heterozygous C→G transition in PTPRC.	We speculate that the mutation may affect activation, adhesion or migration of immune cells, resulting in alteration of the peripheral and local CNS immune response in those patients.	11101853	Details
EBNA-2	allele	N/A	seminested PCR approach and Sanger sequencing	MS	Disease risk	MS risk significantly correlated with an excess of 1.2 allele and underrepresentation of 1.3B allele.	EBNA2 sequence mutations are known to affect interaction with host proteins.	25740864	Details
IL7R	haplotype	Hap 1, Hap 2, Hap 4	semiquantitative RT-PCR	MS	Treatment risk	Similar to our previous findings in CD4 T cells, IL7Rα Hap 4 was not upregulated in response to IFNβ in any of the subsets. In contrast, Hap 1 was upregulated in all subsets in response to IFNβ, and mean Hap 2 IL7Rα levels were increased in all subsets. As a result, Hap 4 was consistently expressed at the lowest level of all the haplotypes in all IFNβ-treated cells, significantly lower than Hap 1 and Hap 2 in maturing DCs. In response to IFNβ, IL7Rα Hap 4 transcript (rs3194051 ‘G’) was expressed at a relatively lower level compared to Hap 1 or Hap 2 (both rs3194051 ‘A’) than in the absence of IFNβ. A significant proportion of the combined cohort decreased relative expression of Hap4 in response to IFNβ when the 3 cell subsets were included in the analysis; this did not reach significance for individual groups or cell subsets, The trend was the same in MS and controls.	We found an association of the interleukin-7 receptor α chain (IL7Rα) with MS and have identified key functional differences between IL7Rα haplotypes that are likely to affect MS susceptibility.IL7Rα is a subunit of receptors for IL-7 and thymic stromal lymphopoietin (TSLP) and is expressed on T cells, dendritic cells (DCs) and other myeloid cells.IL-7 is a critical and nonredundant cytokine mediating survival and differentiation of T cells and their progenitors.IL7Rα has four major haplotypes.Haplotype 2 (Hap 2) is protective against MS and cells exhibit reduced splicing of exon 6 from the transcript, producing less of a soluble isoform (sIL7Rα).IL7Rα signaling exerts powerful effects on myeloid cell function, dependent on the microenvironment and on differentiation status.	24147013	Details
HLA-DRB1	allele	N/A	sequence-specific oligonucleotide (SSO) method	MS	Phenotypic risk	There was no significant association between other HLA-DRB1 alleles and disease course.	Human leucocyte antigen (HLA) complex on chromosome 6p21 is the only locus that has consistently been shown to be associated with MS.	17662002	Details
HLA-A	allele	N/A	sequence-specific oligonucleotide (SSO) method	MS	Phenotypic risk	This study could not identify any significant contribution from HLA-A on the clinical phenotype in MS.	Human leucocyte antigen (HLA) complex on chromosome 6p21 is the only locus that has consistently been shown to be associated with MS.	17662002	Details
HLA-DRB1	HLA-DRB1 *0801 allele	N/A	sequencing-based method	MS	Disease risk	HLA-DRB1 *1501 was strongly associated with both LOMS and EOMS compared to the Control subjects, while HLA-DRB1 *0801 was over-represented in patients with LOMS.	N/A	20580995	Details
HLA-DRB1	polymorphism	HLADRB1*04:01, *04:08, *16:01	sequencing-based typing using generic sequencing of exon 2	MS	Disease risk	In the discovery and validation cohorts, HLADRB1*04:01, *04:08, *16:01 were identified as genetic markers that are associated with an increased risk of anti-interferon beta antibody development (P.05).	N/A	21482927	Details
HLA-DRB1	polymorphism	HLA-DRB1*03:01, *04:04, *11:04	sequencing-based typing using generic sequencing of exon 2	MS	Disease risk	In addition, alleles with a protective potential were identified, including HLA-DRB1*03:01, *04:04, *11:04. However, after correction for multiple testing, protective alleles did not reach statistical significance.	N/A	21482927	Details
DLG5	SNP	rs1248696	Sequenom MassArray MALDI-TOF	MS	N/A	In terms of DLG5, the risk allele is found at a frequency of 0.10 in our MS sample and 0.16 in the SLE sample and was not associated with either disease.	N/A	16642031	Details
IL7R	SNP	rs987107	Sequenom MassARRAY system	MS	Disease risk	In this study, MS patients who had vitamin D deficiency at disease onset exhibited strong association with three SNPs of IL7R; rs987107 (P-value=0.047), rs3194051 (P-value=0.03,) and rs1494571 (P-value=0.036).	N/A	32111053	Details
IL7R	SNP	rs3194051	Sequenom MassARRAY system	MS	Disease risk	In this study, MS patients who had vitamin D deficiency at disease onset exhibited strong association with three SNPs of IL7R; rs987107 (P-value=0.047), rs3194051 (P-value=0.03,) and rs1494571 (P-value=0.036).	N/A	32111053	Details
IL7R	SNP	rs1494571	Sequenom MassARRAY system	MS	Disease risk	In this study, MS patients who had vitamin D deficiency at disease onset exhibited strong association with three SNPs of IL7R; rs987107 (P-value=0.047), rs3194051 (P-value=0.03,) and rs1494571 (P-value=0.036).	N/A	32111053	Details
CD40	SNP	rs1883832	Sequenom MassARRAY system	MS	Disease risk	in addition to two SNPs of CD40, namely rs1883832 and rs6074022 (P-value = 0.049 for both).	N/A	32111053	Details
CD40	SNP	rs6074022	Sequenom MassARRAY system	MS	Disease risk	in addition to two SNPs of CD40, namely rs1883832 and rs6074022 (P-value = 0.049 for both).	N/A	32111053	Details
TAP2	locus	N/A	slot-blotted	MS	N/A	This study shows that MS is not associated to alleles of the TAP2 locus, which is located close to DQ on its centromeric side.	N/A	8071104	Details
CTLA4	SNP	1577 GG	SNaPshotTM Multiplex Kit	MS	Disease risk	SNPs at 1577, +6230, +10242, +10717 and +12310 influence CTLA4 expression and the combination of the 1577 GG and +6230 GG genotypes provokes the strongest decrease in CTLA4 gene expression	N/A	18691768	Details
CTLA4	SNP	+6230	SNaPshotTM Multiplex Kit	MS	Disease risk	SNPs at 1577, +6230, +10242, +10717 and +12310 influence CTLA4 expression and the combination of the 1577 GG and +6230 GG genotypes provokes the strongest decrease in CTLA4 gene expression	N/A	18691768	Details
CTLA4	SNP	+10242	SNaPshotTM Multiplex Kit	MS	Disease risk	SNPs at 1577, +6230, +10242, +10717 and +12310 influence CTLA4 expression and the combination of the 1577 GG and +6230 GG genotypes provokes the strongest decrease in CTLA4 gene expression	N/A	18691768	Details
CTLA4	SNP	+10717	SNaPshotTM Multiplex Kit	MS	Disease risk	SNPs at 1577, +6230, +10242, +10717 and +12310 influence CTLA4 expression and the combination of the 1577 GG and +6230 GG genotypes provokes the strongest decrease in CTLA4 gene expression	N/A	18691768	Details
CTLA4	SNP	+12310	SNaPshotTM Multiplex Kit	MS	Disease risk	SNPs at 1577, +6230, +10242, +10717 and +12310 influence CTLA4 expression and the combination of the 1577 GG and +6230 GG genotypes provokes the strongest decrease in CTLA4 gene expression	N/A	18691768	Details
CTLA4	SNP	-658	SNaPshotTM Multiplex Kit	MS	Disease risk	We found that the SNP at 658 only acted as a regulatory SNP in patients with MS, suggesting the existence of epigenetic changes due to this disease.	N/A	18691768	Details
HLA-DRB1	SNP	rs9271366	SNPline method	MS	Disease risk	We identified a significant interaction between HLA-DR15 in predicting an FCD of CNS demyelination.	N/A	26199349	Details
TRB	rearrangement	N/A	Southern blot	MS	Disease risk	Thus, the human T-cell response to myelin basic protein is exceedingly heterogeneous, even among T cells that recognize the same small fragment of the molecule in association with the same class I1 restriction element.	N/A	1710434	Details
Tcrb	SNP	Vβ8	Southern blot	EAE	disease risk	Our results demonstrate that an mAb specific for the TCR Vβ8 subfamily is effective in preventing autoimmune encephalomyelitis .	Our findings indicate that there is restricted TCRVβ usage in the autoimmune Tcell response to the dominant encephalitogenic NH2-terminal epitope of the MBP.	2452856	Details
TRB	gene rearrangement	N/A	Southern blot	MS	disease risk	Southern blot analysis of the D N A of these T cell clones indicated that all had rearrangements of the TcR β chain genes, but none of the rearrangements were identical.	N/A	3298316	Details
Tcrb	allele	TcR Vβ，TcR Cβ	Southern blots,RFLP	EAE	Disease risk	TcR beta allele from the susceptible strain was present in three out of four susceptible rats, suggesting that it is an important, but not the only, genetic factor in EAE.12 of 13 rats with homozygous LER-derived TCR beta alleles were resistant to EAE.	Coding region differences contribute to a change in function of these TcR molecules, such structural changes could lead to a loss of pathogenicity of the Tcells bearing them.	1716210	Details
MOG	restriction fragment length polymorphism (RFLP)	1.9 kb Taq 1	Southern blotting	MS	Disease risk	None of these distribution of the Taq1 digest polymorphic bands between patients with multiple sclerosis and controls in the present study differences were statistically significant.The incidence in the two sets of patients with multiple sclerosis is very similar.	The lesions of multiple sclerosis are most often held to be caused by an immune attack on CNS myelin.The nature of the antigens involved remains obscure, but peptides from at least two major myelin proteins—myelin basic protein and proteolipid protein—are known to cause cell mediated demyelination in animals (experimental allergic encephalomyelitis) which in some ways resembles human multiple sclerosis.Minor myelin components may presumably also act as autoantigens.Myelin oligodendrocyte glycoprotein (MOG) is a quantitatively minor myelin protein localised to oligodendrocyte cell bodies and processes and to the outer layer of CNS myelin sheaths.In common with several other members of this family, MOG has a membrane spanning domain and an extracellular glycosylated N-terminus and its presence on the outermost surface of myelin and the oligodendrocyte plasma membrane may make MOG accessible to the immune system.	9436746	Details
TNF	gene polymorphism	N/A	southern blotting	MS	Disease risk	the frequency of the NcoI marker phenotypes did not differ between healthy controls and the two disease groups. No extra or missing DNA fragments were observed in the disease groups when compared with controls.	N/A	1969423	Details
IL18	SNP	IL-18 -137C/G and -607C/A	SS-PCR	MS	Disease risk	IL-18 -607AA genotype indicated 6 times higher risk in the development of MS . Smoking seems to be an important confounding factor in MS patients with carrying IL-18 -607 AA and CA+AA genotypes. However, no meaningful association was found with IL-18 -137C/G gene promoter polymorphism.	IL18, is encoded by the IL18 gene, which induces severe inflammatory reactions. An important role of IL-18 has been shown in clinical implications such as elevated serum IL-18 levels in inflammatory as well as some autoimmune diseases including MS .A change at position -137 from G to C alters the H4TF-1 nuclear factor binding site, whereas a change from C to A at position -607 disrupts a potential cAMP-responsive element-binding protein binding site.	27177146	Details
NFKBIL1	Gene polymorphisms	exon 4	SSCP	MS	Disease risk	lack of statistical significance in the two latter parameters suggests insufficient size of the patients and control groups, as the absolute percentage values were remarkably different	NFKBIL1 gene (locus 6p21.31) is one of candidate genes	20568399	Details
HLA-DRB1	Gene polymorphisms	DRB1*1501	SSP-PCR	MS	Disease risk	HLA-DRB1*1501 allele was more frequent among patients	It is believed that genes encoding HLA molecule and cytokines are involved in the pathogenesis of MS	21396892	Details
TNF	Gene polymorphisms	TNF-alpha -308 G/A	SSP-PCR	MS	Disease risk	TNF-α -308 G allele and G/G genotype had higher frequency among MS patients than control subjects	It is believed that genes encoding HLA molecule and cytokines are involved in the pathogenesis of MS	21396892	Details
FOXP3	SNP	rs3761548	SSP-PCR	MS	Disease risk	The frequencies of AA and AC genotypes at rs3761548 in the FOXP3 gene were significantly higher in MS group as compared with healthy subjects (P < 0.05). The frequency of CC genotype at rs3761548 was significantly lower in the MS group in comparison with healthy control subjects (P < 0.001). Moreover, the frequency of A allele was significantly higher whereas the frequency of C allele was significantly lower in MS patients in comparison to healthy subjects (P < 0.001)	The SNP rs3761548 may influence the susceptibility to MS disease	25326790	Details
IL2	allele	IL-2 330 T/HLA-DRB1*1501	SSP-PCR	MS	Disease risk	Our findings support previous findings about the role of the HLA-DRB1*1501 allele in susceptibility to MS.	gene–gene interactions	20594918	Details
HLA-DRB1	allele	HLA-DRB1*15 +/-	SSP-PCR	MS	Disease risk	MS patients carrying HLA-DRB1*15 allele were more frequently born in December.Controls carrying HLA-DRB1*15 allele were less frequently born in December than non-carrier controls.Thus, December was confirmed as the common month of birth for HLA-DRB1*15-non-carrier controls and MS HLA-DRB1*15-carrier patients.	N/A	27569565	Details
IL1A	SNP	rs1800587	SSP-PCR	MS	Disease risk	No association was found with IL1A-889 variants.	The autoimmune inflammatory response in MS is initiated by autoreactive T lymphocytes that mount exaggerated immune responses against autoantigens of the CNS and promote inflammation, demyelination, gliosis and neuroaxonal degeneration.However, it has been demonstrated that lymphocyte migration across the blood–brain barrier is regulated by activation of proinflammatory cytokines, which showed upregulated levels in cerebrospinal fluid (CSF) and sera of MS patients.IL-1 is presented by super-family of immunomodulatory cytokines and natural antagonists that have pleiotropic effects and exert a prominent role in pathogenesis of several auto-inflammatory conditions including MS. IL1α and IL-1β, key members of IL-1 family, are proinflammatory mediators and their pathophysiological impact on the CNS and progression of chronic neurodegenerative diseases has been suggested.In MS, high levels of both cytokines have been found in white matter lesions, and accordingly, the impact of IL-1α and IL-1β on immunopathology of MS has been augmented.	32590124	Details
HLA-DRB1	allele	N/A	SSP-PCR	MS	Disease risk	Results showed the presence of a significantly higher frequency of -DRB1-11 alleles in HC compared to MS patients. Conversely DRB1-15 was more frequent in MS patients then in HC.The distribution of the frequencies of the other HLA-DRB1 alleles was not different between patients and controls.	N/A	21664963	Details
IL1B	SNP	rs16944	SSP-PCR	MS	Disease risk	Under dominant model, IL1B511 CT + TT genotype was significantly associated with a decreased MS risk.Frequencies of IL1B511 T variant alleles were significantly decreased in MS patients compared to control.	The autoimmune inflammatory response in MS is initiated by autoreactive T lymphocytes that mount exaggerated immune responses against autoantigens of the CNS and promote inflammation, demyelination, gliosis and neuroaxonal degeneration.However, it has been demonstrated that lymphocyte migration across the blood–brain barrier is regulated by activation of proinflammatory cytokines, which showed upregulated levels in cerebrospinal fluid (CSF) and sera of MS patients.IL-1 is presented by super-family of immunomodulatory cytokines and natural antagonists that have pleiotropic effects and exert a prominent role in pathogenesis of several auto-inflammatory conditions including MS. IL1α and IL-1β, key members of IL-1 family, are proinflammatory mediators and their pathophysiological impact on the CNS and progression of chronic neurodegenerative diseases has been suggested.In MS, high levels of both cytokines have been found in white matter lesions, and accordingly, the impact of IL-1α and IL-1β on immunopathology of MS has been augmented.	32590124	Details
IL1B	SNP	rs1143634	SSP-PCR	MS	Disease risk	No association was found with IL1B+3962 variants.	The autoimmune inflammatory response in MS is initiated by autoreactive T lymphocytes that mount exaggerated immune responses against autoantigens of the CNS and promote inflammation, demyelination, gliosis and neuroaxonal degeneration.However, it has been demonstrated that lymphocyte migration across the blood–brain barrier is regulated by activation of proinflammatory cytokines, which showed upregulated levels in cerebrospinal fluid (CSF) and sera of MS patients.IL-1 is presented by super-family of immunomodulatory cytokines and natural antagonists that have pleiotropic effects and exert a prominent role in pathogenesis of several auto-inflammatory conditions including MS. IL1α and IL-1β, key members of IL-1 family, are proinflammatory mediators and their pathophysiological impact on the CNS and progression of chronic neurodegenerative diseases has been suggested.In MS, high levels of both cytokines have been found in white matter lesions, and accordingly, the impact of IL-1α and IL-1β on immunopathology of MS has been augmented.	32590124	Details
IL1R1	SNP	rs2234650	SSP-PCR	MS	Disease risk	Under dominant model, IL1R1pst1970CT + TT genotype was significantly associated with a decreased MS risk.IL1R1pst1 1970 T variant alleles were significantly decreased in MS patients compared to control.	The autoimmune inflammatory response in MS is initiated by autoreactive T lymphocytes that mount exaggerated immune responses against autoantigens of the CNS and promote inflammation, demyelination, gliosis and neuroaxonal degeneration.However, it has been demonstrated that lymphocyte migration across the blood–brain barrier is regulated by activation of proinflammatory cytokines, which showed upregulated levels in cerebrospinal fluid (CSF) and sera of MS patients. Interleukin-1 receptor antagonist (IL1-RA) is the naturally occurring antagonist of IL-1α/IL-1β signaling pathways.It competitively inhibits both cytokines by binding the IL-1 receptor type I (IL-1R1).	32590124	Details
IL1RN	SNP	rs315952	SSP-PCR	MS	Disease risk	Under dominant model, IL1RNmspa1 11,100 TC + CC genotype was significantly associated with a decreased MS risk.The heterozygous genotype TC of the variant was also associated with a significant decreased MS risk but under codominant model.Frequencies of IL1RNmspa1 11,100C variant alleles were significantly decreased in MS patients compared to control.	The autoimmune inflammatory response in MS is initiated by autoreactive T lymphocytes that mount exaggerated immune responses against autoantigens of the CNS and promote inflammation, demyelination, gliosis and neuroaxonal degeneration.However, it has been demonstrated that lymphocyte migration across the blood–brain barrier is regulated by activation of proinflammatory cytokines, which showed upregulated levels in cerebrospinal fluid (CSF) and sera of MS patients.	32590124	Details
MMP9	polymorphisms	MMP-9 -1562 C/T	SSP-PCR	MS	Disease risk	A significant decrease of the -1562T allele carriers in MS patients compared to controls in -1562C/T MMP-9 gene polymorphism was found.Significant differences were also demonstrated between female patients and healthy females.	The migration of autoreactive immune cells through the BBB into the CNS is crucial to the formation of inflammatory MS lesions.An important role in this process is played by matrix metalloproteinases (MMPs).In multiple sclerosis, they are assumed to act as effector molecules in the disruption of the BBB, invasion of inflammatory cells into the CNS parenchyma and degradation of myelin basic protein (MBP).	18835646	Details
IL10	SNP	IL-10 -1082 G/G and IL-10 -819 C/C	SSP-PCR	MS	Disease risk	It was found that IL-10 1082 G/G genotype was associated with higher risk of MS in Iranian population, while G/A and A/A genotypes reduced the risk of the disease and 819 CC genotype was also associated with higher risk of developing MS.	Interleukin 10 (IL-10) is an anti-inflammatory cytokine and the amount of IL-10 production has a direct association with the progression or recovery of MS . The three SNPs in the promoter region of IL-10 gene, 1082 G/A, 819 T/C and 592 A/C, have been shown to be in association with high or low production of this cytokine.	29067976	Details
HLA-DRB1	SNP	HLA-DRB1*15	SSP-PCR	MS	Disease risk	DRB1*15 allele showed a higher frequency among MS patients as compared with control subjects.	N/A	29067976	Details
PTPRC	C77G	N/A	subsequent dot-blot analysi	MS	N/A	We concluded that, despite the presence of CD45 G77 polymorphism in a few patients who did not carry the HLADR- DQ MS-predisposing molecules, CD45 did not contribute to development of the disease in Sardinian MS.	N/A	15372250	Details
GAS5	SNP	rs2067079	T-ARMS-PCR	MS	Disease risk	There was a significant over-representation of the rs2067079 T allele in MS patients compared with healthy individuals .This SNP was associated with MS risk in co-dominant and recessive models.	The T allele of the rs2067079 would change the secondary structure of the transcript and upsurge the minimum free energy. Notably this SNP alters the binding site for a number of microRNAs.	30790644	Details
GAS5	SNP	rs6790	T-ARMS-PCR	MS	Disease risk	The rs6790 was not associated with MS risk in any inheritance models.	N/A	30790644	Details
EBF1	SNP	rs1368297	Taq polymerase	MS	Disease risk	Our data support EBF1 gene association with MS pathogenesis in the Spanish white population. Two genetic markers within the EBF1 gene have been found associated with this neurological disease, indicative either of their causative role or that of some other polymorphism in linkage disequilibrium with them.	Our data suggest that the EBF1 gene involved in B-cell development, adipogenesis and axonal damage play a causative role in MS. Many mechanistic ties between axonal damage, tau pathology, intrathecal B1 subpopulation responsible for IgM secretion, conventional B cells, and the EBF1 gene role in MS susceptibility could be thought up. Confirmation in an independent cohort would substantiate our hypothesis about the implications of this gene in MS.	16255771	Details
IL7R	SNP	rs11567685	Taq polymerase,PCR	MS	Disease risk	Meanwhile, a significant difference was detected between control and primary progressive MS patients considering promoter SNPrs11567685 marker frequency. Also, a significant difference was detected considering exonic SNPrs6897932 for secondary progressive MS patients.	N/A	21190413	Details
IL7R	SNP	rs6897932	Taq polymerase,PCR	MS	Disease risk	Meanwhile, a significant difference was detected between control and primary progressive MS patients considering promoter SNPrs11567685 marker frequency. Also, a significant difference was detected considering exonic SNPrs6897932 for secondary progressive MS patients.	N/A	21190413	Details
CD6	SNP	rs11230563	Taq polymerase,PCR	MS	Disease risk	CD6, CLEC16a, EVI5, GPC5, and TYK2 contained SNPs that are associated with MS risk in the African American data set.	Allelic variants at rs11230563 may result in altered activation of T cells, thereby affecting an individual’s susceptibility to MS.	19865102	Details
CLEC16A	SNP	rs12708716	Taq polymerase,PCR	MS	Disease risk	CD6, CLEC16a, EVI5, GPC5, and TYK2 contained SNPs that are associated with MS risk in the African American data set.	Although the function of CLEC16a is unknown, CLEC16a is expressed on B cells, dendritic cells, and natural killer cells.	19865102	Details
CLEC16A	SNP	rs6498169	Taq polymerase,PCR	MS	Disease risk	CD6, CLEC16a, EVI5, GPC5, and TYK2 contained SNPs that are associated with MS risk in the African American data set.	Although the function of CLEC16a is unknown, CLEC16a is expressed on B cells, dendritic cells, and natural killer cells.	19865102	Details
EVI5	SNP	rs10735781	Taq polymerase,PCR	MS	Disease risk	CD6, CLEC16a, EVI5, GPC5, and TYK2 contained SNPs that are associated with MS risk in the African American data set.	Allelic differences in EVI5 may contribute to altered function of RAB11 and altered formation of the immunological synapse, thus contributing to MS susceptibility.	19865102	Details
EVI5	SNP	rs6680578	Taq polymerase,PCR	MS	Disease risk	CD6, CLEC16a, EVI5, GPC5, and TYK2 contained SNPs that are associated with MS risk in the African American data set.	Allelic differences in EVI5 may contribute to altered function of RAB11 and altered formation of the immunological synapse, thus contributing to MS susceptibility.	19865102	Details
GPC5	SNP	rs553717	Taq polymerase,PCR	MS	Disease risk	CD6, CLEC16a, EVI5, GPC5, and TYK2 contained SNPs that are associated with MS risk in the African American data set.	Allelic variants of GPC5 may affect neuronal repair and contribute to differences in MS susceptibility.	19865102	Details
TYK2	SNP	rs34536443	Taq polymerase,PCR	MS	Disease risk	CD6, CLEC16a, EVI5, GPC5, and TYK2 contained SNPs that are associated with MS risk in the African American data set.	N/A	19865102	Details
HLA-DRB1	HLA-DR15	N/A	TaqI-digested, Southern-blot	MS	Disease risk	We found that, in addition to DR15, DR17 is positively associated with susceptibility to MS; that none of the HLA-DRB1 alleles influences course or outcome in MS; that carriers of DR15 are prone to MS development at an earlier age than noncarriers; and that differences in DR15 positivity rates, after stratification for diagnostic category and examination results, seem to reflect a gradient of phenocopy contamination, with rates increasing in proportion to the degree of clinical or paraclinical verification of the MS diagnosis.	N/A	10939572	Details
SIRT1	SNP	rs3758391	TaqMan	MS	Disease risk	There was no association between SIRT1 levels and ON with/ without MS development.	N/A	36949521	Details
SIRT1	SNP	rs7895833	TaqMan	MS	Disease risk	There was no association between SIRT1 levels and ON with/ without MS development.	N/A	36949521	Details
SOCS1	SNP	rs243324	Taqman	MS	Disease risk	The SOCS1 rs243324 variant was validated as risk factor for MS	The association with SOCS1 appears independent from the chr16MS risk locus CLEC16A	21716315	Details
CD6	SNP	rs12288280	TaqMan	MS	Disease risk	one SNP in CD6 (rs12288280, P = 0.04) and three SNPs in TNFRSF1A (rs767455, rs4149577, and rs1800693, P = 0.01-0.03) were associated with NMO	were predicted to be binding sites for splicing factors	22994200	Details
TNFRSF1A	SNP	rs767455	TaqMan	MS	Disease risk	one SNP in CD6 (rs12288280, P = 0.04) and three SNPs in TNFRSF1A (rs767455, rs4149577, and rs1800693, P = 0.01-0.03) were associated with NMO	were predicted to be binding sites for splicing factors	22994200	Details
TNFRSF1A	SNP	rs1800693	TaqMan	MS	Disease risk	one SNP in CD6 (rs12288280, P = 0.04) and three SNPs in TNFRSF1A (rs767455, rs4149577, and rs1800693, P = 0.01-0.03) were associated with NMO	were predicted to be binding sites for splicing factors	22994200	Details
TNFRSF1A	SNP	rs4149577	TaqMan	MS	Disease risk	one SNP in CD6 (rs12288280, P = 0.04) and three SNPs in TNFRSF1A (rs767455, rs4149577, and rs1800693, P = 0.01-0.03) were associated with NMO	were predicted to be binding sites for splicing factors	22994200	Details
IRF8	SNP	rs767455	TaqMan	MS	Disease risk	there was no association of IRF8 polymorphisms with IDD, including MS and NMO	N/A	22994200	Details
STAT4	SNP	rs7574865	TaqMan	MS	Disease risk	The STAT4 gene is emerging as a novel common risk factor for diverse complex diseases.	The STAT4 gene encodes a transcription factor involved in the signaling pathways of several cytokines, including interleukin-12 (IL-12), the type I interferons, and IL-23.	18759272	Details
GSTP1	SNP	rs1695	TaqMan	MS	N/A	Among MS patients, there was no relationship between the rs1695 variant and either gender, clinical type of MS or the age of onset of MS.	N/A	25531394	Details
HLA-G	a 14 bp insertion / deletion in the untranslated exon 8	N/A	TaqMan	MS	N/A	No association was seen with the age of onset of disease, disease severity or disease course. Although HLA-G is assumed to play an important role in the immunoregulatory processes of MS, our results do not support a role of genetic factors influencing disease susceptibility of the disease course.	N/A	17462509	Details
ZC3HAV1	SNP	rs3735007	Taqman	MS	Disease risk	The selective pressure is likely to be virus driven; in modern populations, this variant associates with susceptibility to MS, possibly via the interaction with environmental factors.	via the interaction with environmental factors.	22319148	Details
HLA-G	The -725 C/G exchange in the HLA-G promoter region	N/A	TaqMan	MS	N/A	No association was seen with the age of onset of disease, disease severity or disease course. Although HLA-G is assumed to play an important role in the immunoregulatory processes of MS, our results do not support a role of genetic factors influencing disease susceptibility of the disease course.	N/A	17462509	Details
HLA-G	HLA-G*0105N, a deletion that results in an irregular stopcodon in exon 3	N/A	TaqMan	MS	N/A	No association was seen with the age of onset of disease, disease severity or disease course. Although HLA-G is assumed to play an important role in the immunoregulatory processes of MS, our results do not support a role of genetic factors influencing disease susceptibility of the disease course.	N/A	17462509	Details
L3MBTL3	SNP	rs7740107	TaqMan	MS	Disease risk	Our data and other functional studies suggest that the genetic mechanism underlying the MS association of rs7740107 affects not only the expression of L3MBTL3 isoforms, but might also involve the Notch signalling pathway.	Our data and other functional studies suggest that the genetic mechanism underlying the MS association of rs7740107 affects not only the expression of L3MBTL3 isoforms, but might also involve the Notch signalling pathway.	35088080	Details
IDO2	SNP	rs10109853	TaqMan	MS	N/A	IDO2 rs10109853 and rs4503083 polymorphisms are not associated with MS risk, age at onset and disease progression in Italian MS patients.	N/A	28477703	Details
IDO2	SNP	rs4503083	TaqMan	MS	N/A	IDO2 rs10109853 and rs4503083 polymorphisms are not associated with MS risk, age at onset and disease progression in Italian MS patients.	N/A	28477703	Details
CASP8	SNP	rs2037815	TaqMan	MS	Disease risk	GG homozygosity for SNP rs2037815 in PPMS patients was associated with a trend towards faster disease progression.	N/A	20363033	Details
IL2RA	SNP	rs1570538	TaqMan	MS	Disease risk	These findings confirm and extend the association of this gene with MS and reveal a genetic heterogeneity of the associated polymorphisms and risk alleles between MS and T1D suggesting different immunopathological roles of IL2RA in these two diseases.	immunopathological roles	19125193	Details
CASP8	SNP	rs12990906	TaqMan	MS	Disease risk	For SNP rs12990906, CT heterozygosity was associated with PPMS when compared with controls (OR= 1.9; corrected p-value= 0.030).	N/A	20363033	Details
IL2RA	SNP	rs2104286	TaqMan	MS	Disease risk	These findings confirm and extend the association of this gene with MS and reveal a genetic heterogeneity of the associated polymorphisms and risk alleles between MS and T1D suggesting different immunopathological roles of IL2RA in these two diseases.	immunopathological roles	19125193	Details
CASP8	SNP	rs13113	TaqMan	MS	Disease risk	For SNP rs13113, no significant associations at the allele or genotype levels were found between MS patients with different clinical forms and controls.	N/A	20363033	Details
IL2RA	SNP	rs12722489	TaqMan	MS	Disease risk	These findings confirm and extend the association of this gene with MS and reveal a genetic heterogeneity of the associated polymorphisms and risk alleles between MS and T1D suggesting different immunopathological roles of IL2RA in these two diseases.	immunopathological roles	19125193	Details
IL2RA	SNP	rs10795791	TaqMan	MS	Disease risk	These findings confirm and extend the association of this gene with MS and reveal a genetic heterogeneity of the associated polymorphisms and risk alleles between MS and T1D suggesting different immunopathological roles of IL2RA in these two diseases.	immunopathological roles	19125193	Details
IL2RA	SNP	rs4147359	TaqMan	MS	Disease risk	These findings confirm and extend the association of this gene with MS and reveal a genetic heterogeneity of the associated polymorphisms and risk alleles between MS and T1D suggesting different immunopathological roles of IL2RA in these two diseases.	immunopathological roles	19125193	Details
IL2RA	SNP	rs7090530	TaqMan	MS	Disease risk	These findings confirm and extend the association of this gene with MS and reveal a genetic heterogeneity of the associated polymorphisms and risk alleles between MS and T1D suggesting different immunopathological roles of IL2RA in these two diseases.	immunopathological roles	19125193	Details
IL2RA	SNP	rs41295061	TaqMan	MS	Disease risk	These findings confirm and extend the association of this gene with MS and reveal a genetic heterogeneity of the associated polymorphisms and risk alleles between MS and T1D suggesting different immunopathological roles of IL2RA in these two diseases.	immunopathological roles	19125193	Details
IL2RA	SNP	rs35285258	TaqMan	MS	Disease risk	These findings confirm and extend the association of this gene with MS and reveal a genetic heterogeneity of the associated polymorphisms and risk alleles between MS and T1D suggesting different immunopathological roles of IL2RA in these two diseases.	immunopathological roles	19125193	Details
ERAP1	SNP	rs30187	TaqMan	MS	Disease risk	In summary, we report that a functional ERAP1 allele previously associated to AS confers susceptibility to MS in Italian populations, whereas its role in predisposing to CD remains to be evaluated.	N/A	22253828	Details
GRN	SNP	rs2879096	TaqMan	MS	Disease risk	An association with the rs2879096T allele was observed (29.2 in patients compared with 18.9% in controls, P=0.012, OR 1.77, 95% CI 1.1-2.8).	N/A	20463744	Details
CIITA	SNP	rs4774	TaqMan	MS	Disease risk	Rs4774 (missense +1614G/C; G500A) was associated with MS (P = 4.9 x 10(-3)), particularly in DRB1*1501 +individuals (P = 1 x 10(-4)).	N/A	20211854	Details
CD33	SNP	rs3865444	TaqMan	MS	Disease risk	Therefore, we could assume that the CD33 rs3865444 GG genotype predisposes towards MS by increasing CD33 cell surface expression and decreasing the alternatively spliced CD33m variant, thus altering myeloid cells function.	Therefore, we could assume that the CD33 rs3865444 GG genotype predisposes towards MS by increasing CD33 cell surface expression and decreasing the alternatively spliced CD33m variant, thus altering myeloid cells function.	33198164	Details
TNFRSF1A	SNP	rs1800693	TaqMan	MS	Disease risk	By analysing MS GWAS data in conjunction with the 1000 Genomes Project data we provide genetic evidence that strongly implicates this SNP, rs1800693, as the causal variant in the TNFRSF1A region.	N/A	22801493	Details
CTLA4	SNP	rs3087243	TaqMan	MS	Disease risk	A common variant within CTLA4 was strongly associated with multiple sclerosis in families who had other autoimmune diseases (p=0.009) but not in families without a history of other autoimmune disorders (p=0.90).	N/A	17052659	Details
HLA-DRB1	SNP	DRB1*1503	TaqMan	MS	Disease risk	Although significant associations with both HLA-DRB1 and HLA-DRB5 loci were present, HLA-DRB1*1503 was associated with MS in the absence of HLA-DRB5, providing evidence for HLA-DRB1 as the primary susceptibility gene	MS is associated with the MHC located on chromosome 6p21	18832704	Details
HLA-DRB5	SNP	DRB5*null	TaqMan	MS	Disease risk	the HLA-DRB5*null subjects appear to be at increased risk for developing secondary progressive MS	MS is associated with the MHC located on chromosome 6p21	18832704	Details
AGER	SNP	rs1035798	TaqMan	MS	Disease risk	Both AGER SNPs showed evidence for association when conditioned on the DRB1 genotype using WHAP (p < 0.01 for rs1035798 in African Americans and p < 0.0001 for rs2070600 in whites, data not shown), which were similar to results shown for the conditional haplotype analysis (Tables IV and andVI).VI). This is compatible with independent contributions from both AGER and DRB1 to MS susceptibility	conditional haplotype analysis revealed a susceptibility signal at the class III AGER locus independent of DRB1	18832704	Details
AGER	SNP	rs2070600	TaqMan	MS	Disease risk	Both AGER SNPs showed evidence for association when conditioned on the DRB1 genotype using WHAP (p < 0.01 for rs1035798 in African Americans and p < 0.0001 for rs2070600 in whites, data not shown), which were similar to results shown for the conditional haplotype analysis (Tables IV and andVI).VI). This is compatible with independent contributions from both AGER and DRB1 to MS susceptibility	conditional haplotype analysis revealed a susceptibility signal at the class III AGER locus independent of DRB1	18832704	Details
LRP2	SNP	rs12988804	TaqMan	MS	Disease risk	The LRP2 risk allele was associated with decreased performance on the California Verbal Learning Test 2 after correction (CC vs. CT+TT 95% CI -14.2--3.4, p = 0.0018).	N/A	34678704	Details
SIRPG	SNP	rs2281808	TaqMan	MS	Disease risk	As compared to HD, RRMS and T1D patients show significantly greater preponderance of rs2281808 CT/TT carriers.	Interestingly, increased frequencies of SIRPγlow T-cells in RRMS and T1D positively correlated with proinflammatory molecules from T-cells.	32853219	Details
VDR	FokI ff	N/A	TaqMan	MS	Disease risk	A statistically significant higher frequency of the ff genotype was observed in MS patients (15.6% vs. 10.1%, p=0.012, OR (95% CI)=1.687(1.120-2.541)).	N/A	28601283	Details
IL12B	SNP	rs6887695	TaqMan	MS	Disease risk	The rs6887695 single-nucleotide polymorphism (SNP) in IL12B gene showed an association with susceptibility to MS	N/A	28276258	Details
CSGALNACT1	cSNP	rs140161612	TaqMan	MS	N/A	No significant difference was observed between controls and MS. No significant difference also was observed in the ChGn-1 SNP frequencies among MS subtypes.	This cSNP might be associated with the sex differences in clinical course of MS.	26806424	Details
NQO1	SNP	rs1800566	TaqMan	MS	N/A	NQO1 rs1800566 allelic and genotypic frequencies did not differ significantly between MS patients and controls, and were unrelated with age of onset of MS, gender, and clinical type of MS.	N/A	24755231	Details
CD226	SNP	rs1788229	TaqMan	MS	N/A	However, the significance of rs1788229 disappeared after a multiple testing correction of the data (p>0.05).	However, our results suggest that the causal genes for inflammatory demyelinating diseases may vary depending on the population.	23922043	Details
CD226	SNP	rs763361	TaqMan	MS	N/A	Interestingly, rs763361, which showed significant associations with multiple sclerosis in several previous studies, did not show any association at all.	However, our results suggest that the causal genes for inflammatory demyelinating diseases may vary depending on the population.	23922043	Details
BTG1	SNP	rs731652	TaqMan	MS	Disease risk	For SNP rs731652, significant associations with relapse-onset MS were found at the allele and genotype levels when compared with controls.	N/A	19515430	Details
CIITA	SNP	rs4774	TaqMan ABI 7900	MS	Disease risk	A significant association ofrs4774 (P0.01) was discovered in this analysis;In a logistic regression model with age as a covariate, the association with MS remained for rs4774	The DRB1 locus in the HLA class II region is the major established genetic determinant of disease risk in MS that makes interaction between these loci plausible for any possible association with the CIITA gene	24430172	Details
HLA-DRB1	SNP	DRB1*15:01	TaqMan ABI 7900	MS	Disease risk	We find that the previously investigated single-nucleotide polymorphism rs4774 is associated with MS risk in cases carrying the HLA-DRB1*15 allele	The DRB1 locus in the HLA class II region is the major established genetic determinant of disease risk in MS that makes interaction between these loci plausible for any possible association with the CIITA gene	24430172	Details
IL4	gene are in strong linkage disequilibrium	rs2070874	TaqMan Assay	MS	Disease risk	An MS protective role for the heterozygous genotype was confirmed in Spain	controls transcriptional activity	16169606	Details
VDR	SNP	rs1544410(BsmI)、rs7975232(ApaI)、rs731236(TaqI)、rs10735810(FokI)、rs11568820(Cdx-2)	TaqMan assay	MS	Disease risk	this does not support a role for the selected SNPs involved in vitamin D metabolism in the etiology of MS	N/A	20007432	Details
CYP27B1	SNP	rs703426、rs10877012	TaqMan assay	MS	Disease risk	this does not support a role for the selected SNPs involved in vitamin D metabolism in the etiology of MS	N/A	20007432	Details
CYP24A1	SNP	rs2296241	TaqMan assay	MS	Disease risk	this does not support a role for the selected SNPs involved in vitamin D metabolism in the etiology of MS	N/A	20007432	Details
CYP2R1	SNP	rs10500804, rs12794714	TaqMan assay	MS	Disease risk	this does not support a role for the selected SNPs involved in vitamin D metabolism in the etiology of MS	N/A	20007432	Details
DBP	SNP	rs7041、rs4588	TaqMan assay	MS	Disease risk	this does not support a role for the selected SNPs involved in vitamin D metabolism in the etiology of MS	N/A	20007432	Details
TNFSF13B	SNP	rs374039502	TaqMan assay	N/A	Disease risk	Our data suggest that the TNFSF13B functional variant does not contribute to the genetic network underlying GCA and SSc	The TNFSF13B (TNF superfamily member 13b) gene encodes BAFF, a cytokine with a crucial role in the differentiation and activation of B cells	30586461	Details
HMOX2	SNP	rs1051308AA	TaqMan assays	MS	Disease risk	The frequencies of HMOX2 rs1051308AA genotype and HMOX2 rs1051308A and HMOX1 rs2071746A alleles were higher in MS patients than in controls,	he most likely mechanism would be related to gene expression	26868429	Details
HMOX2	SNP	rs1051308A	TaqMan assays	MS	Disease risk	The frequencies of HMOX2 rs1051308AA genotype and HMOX2 rs1051308A and HMOX1 rs2071746A alleles were higher in MS patients than in controls,	he most likely mechanism would be related to gene expression	26868429	Details
HMOX1	SNP	rs2071746A	TaqMan assays	MS	Disease risk	The frequencies of HMOX2 rs1051308AA genotype and HMOX2 rs1051308A and HMOX1 rs2071746A alleles were higher in MS patients than in controls,	he most likely mechanism would be related to gene expression	26868429	Details
IFIH1	SNP	rs2111485, rs1990760, rs3747517, rs13023380	TaqMan assays, restriction fragment length polymorphism (RFLP) or high resolution melting (HRM) analysis	MS	Disease risk	Evaluation of single nucleotide polymorphisms (SNPs) in the gene did not reveal significant single-SNP associations with MS risk.	Increased activation of RLR genes has been demonstrated in peripheral blood cells of MS patients.It was speculated that genetic alterations in the RIG-I-like receptor signaling pathway may lead to inadequate immune responses and increase the susceptibility for autoimmune disorders.	25288302	Details
RIGI	SNP	rs12555727, rs10813825, rs6476363, rs659527, rs626214	TaqMan assays, restriction fragment length polymorphism (RFLP) or high resolution melting (HRM) analysis	MS	Disease risk	Evaluation of single nucleotide polymorphisms (SNPs) in the gene did not reveal significant single-SNP associations with MS risk.	Increased activation of RLR genes has been demonstrated in peripheral blood cells of MS patients.It was speculated that genetic alterations in the RIG-I-like receptor signaling pathway may lead to inadequate immune responses and increase the susceptibility for autoimmune disorders.	25288302	Details
MAVS	SNP	rs4815617, rs7262903, rs17857295, rs45437096, rs16989000	TaqMan assays, restriction fragment length polymorphism (RFLP) or high resolution melting (HRM) analysis	MS	Disease risk	Evaluation of single nucleotide polymorphisms (SNPs) in the gene did not reveal significant single-SNP associations with MS risk.	Increased activation of RLR genes has been demonstrated in peripheral blood cells of MS patients.It was speculated that genetic alterations in the RIG-I-like receptor signaling pathway may lead to inadequate immune responses and increase the susceptibility for autoimmune disorders.	25288302	Details
IL7R	SNP	rs11567685	TaqMan assays,qRT-PCR	MS	Disease risk	these results confirm involvement of polymorphisms in the IL7RA and IL2RA genes in MS pathogenesis and suggest that IL7RA variation may primarily affect chronic disease courses.	differential splicing	19231135	Details
IL7R	SNP	rs1494555	TaqMan assays,qRT-PCR	MS	Disease risk	these results confirm involvement of polymorphisms in the IL7RA and IL2RA genes in MS pathogenesis and suggest that IL8RA variation may primarily affect chronic disease courses.	differential splicing	19231135	Details
IL7R	SNP	rs6897932	TaqMan assays,qRT-PCR	MS	Disease risk	these results confirm involvement of polymorphisms in the IL7RA and IL2RA genes in MS pathogenesis and suggest that IL9RA variation may primarily affect chronic disease courses.	differential splicing	19231135	Details
IL7R	SNP	rs987106	TaqMan assays,qRT-PCR	MS	Disease risk	these results confirm involvement of polymorphisms in the IL7RA and IL2RA genes in MS pathogenesis and suggest that IL10RA variation may primarily affect chronic disease courses.	differential splicing	19231135	Details
IL7R	SNP	rs3194051	TaqMan assays,qRT-PCR	MS	Disease risk	these results confirm involvement of polymorphisms in the IL7RA and IL2RA genes in MS pathogenesis and suggest that IL11RA variation may primarily affect chronic disease courses.	differential splicing	19231135	Details
IL2RA	SNP	rs12722489	TaqMan assays,qRT-PCR	MS	Disease risk	these results confirm involvement of polymorphisms in the IL7RA and IL2RA genes in MS pathogenesis and suggest that IL12RA variation may primarily affect chronic disease courses.	differential splicing	19231135	Details
IL2RA	SNP	rs2104286	TaqMan assays,qRT-PCR	MS	Disease risk	these results confirm involvement of polymorphisms in the IL7RA and IL2RA genes in MS pathogenesis and suggest that IL13RA variation may primarily affect chronic disease courses.	differential splicing	19231135	Details
IL2RA	SNP	rs11256369	TaqMan assays,qRT-PCR	MS	Disease risk	these results confirm involvement of polymorphisms in the IL7RA and IL2RA genes in MS pathogenesis and suggest that IL14RA variation may primarily affect chronic disease courses.	differential splicing	19231135	Details
IL2RA	SNP	rs7076103	TaqMan assays,qRT-PCR	MS	Disease risk	these results confirm involvement of polymorphisms in the IL7RA and IL2RA genes in MS pathogenesis and suggest that IL15RA variation may primarily affect chronic disease courses.	differential splicing	19231135	Details
TNFRSF1A	SNP	rs767455	Taqman Assays-on-Demand and Taqman Assays-by-Design	MS	Disease risk	No other non-synonymous variants in the same allele frequency range influencing risk of MS were observed.	Patients with the autoinflammatory disease Tumour Necrosis Factor receptor-associated periodic syndrome (TRAPS) who suffer from demyelinating disease have been described, and one of the milder TRAPS mutations (R92Q in the TNFRSF1A gene) has been suggested as a risk factor for multiple sclerosis (MS).	21565411	Details
TNFRSF1A	SNP	rs4149584	Taqman Assays-on-Demand and Taqman Assays-by-Design	MS	Disease risk	which appears independent of an established common risk variant in the same gene.	Patients with the autoinflammatory disease Tumour Necrosis Factor receptor-associated periodic syndrome (TRAPS) who suffer from demyelinating disease have been described, and one of the milder TRAPS mutations (R92Q in the TNFRSF1A gene) has been suggested as a risk factor for multiple sclerosis (MS).	21565411	Details
IRF5	SNP	rs2004640-TT	Taqman Genotyping Assay	MS	Disease risk	We found that patients with the IRF5 rs2004640-TT and rs47281420-AA genotype exerted a poor pharmacological response to IFNb compared with patients carrying the respective G-alleles (P 0.0006 and P 0.0023, respectively). Moreover, patients with the rs2004640-TT genotype developed more magnetic resonance imaging (MRI)-based T2 lesions during IFNb treatment (P 0.003). Accordingly, an association between MRI-based non-responder status and rs2004640-TT genotype was observed (P 0.010). For the rs4728142-AA genotype a trend of an association with more T2 lesions during IFNb treatment and MRI-based non-responder status was observed (P 0.103 and P 0.154, respectively).	Clinical non-responders were characterized by an increased expression of IFN response genes before the start of therapy, and a lack of a pharmacologically induced increase in IFN response gene activity. Because Interferon Regulatory Factor 5 (IRF5) is a master regulator of IFN-activity, we carried out a candidate gene study of IRF5 gene variants in relation to the pharmacological and clinical response upon IFNb treatment	21471993	Details
IRF5	SNP	rs47281420-AA	Taqman Genotyping Assay	MS	Disease risk	We found that patients with the IRF5 rs2004640-TT and rs47281420-AA genotype exerted a poor pharmacological response to IFNb compared with patients carrying the respective G-alleles (P 0.0006 and P 0.0023, respectively). Moreover, patients with the rs2004640-TT genotype developed more magnetic resonance imaging (MRI)-based T2 lesions during IFNb treatment (P 0.003). Accordingly, an association between MRI-based non-responder status and rs2004640-TT genotype was observed (P 0.010). For the rs4728142-AA genotype a trend of an association with more T2 lesions during IFNb treatment and MRI-based non-responder status was observed (P 0.103 and P 0.154, respectively).	Clinical non-responders were characterized by an increased expression of IFN response genes before the start of therapy, and a lack of a pharmacologically induced increase in IFN response gene activity. Because Interferon Regulatory Factor 5 (IRF5) is a master regulator of IFN-activity, we carried out a candidate gene study of IRF5 gene variants in relation to the pharmacological and clinical response upon IFNb treatment	21471993	Details
IRF5	SNP	rs4728142-AA	Taqman Genotyping Assay	MS	Disease risk	We found that patients with the IRF5 rs2004640-TT and rs47281420-AA genotype exerted a poor pharmacological response to IFNb compared with patients carrying the respective G-alleles (P 0.0006 and P 0.0023, respectively). Moreover, patients with the rs2004640-TT genotype developed more magnetic resonance imaging (MRI)-based T2 lesions during IFNb treatment (P 0.003). Accordingly, an association between MRI-based non-responder status and rs2004640-TT genotype was observed (P 0.010). For the rs4728142-AA genotype a trend of an association with more T2 lesions during IFNb treatment and MRI-based non-responder status was observed (P 0.103 and P 0.154, respectively).	Clinical non-responders were characterized by an increased expression of IFN response genes before the start of therapy, and a lack of a pharmacologically induced increase in IFN response gene activity. Because Interferon Regulatory Factor 5 (IRF5) is a master regulator of IFN-activity, we carried out a candidate gene study of IRF5 gene variants in relation to the pharmacological and clinical response upon IFNb treatment	21471993	Details
PRNP	polymorphism	129Val	TaqMan method	MS	Disease risk	Statistical analysis revealed no significant association between PRNP*129Val and MS.	The methionine/valine polymorphism at codon 129 of the prion protein gene (PRNP) have been known risk factors for clinical and pathologic phenotype of both sporadic and familial forms of prion diseases. In MS, the mechanism underlying this association can be traced to the modified prion as a factor initializing immune system reactions against myelin membrane of neuronal axons. A previous study has demonstrated that methionine homozygosity at codon 129 is associated with a reduction in white matter tissue and a larger volume of cerebrospinal fluid in schizophrenic patients.	20592456	Details
NLRP3	SNP	rs3806265	TaqMan method	MS	Disease risk	In this study, we found that NLRP3 rs3806265 C allele and CC genotype were significantly more frequent in the RRMS patients (p value = 0.03 OR = 1.66, 95% CI = 1.14-2.43) and p value = 0.04, OR = 3.26, 95% CI = 1.19-8.93, respectively), while the frequency of T allele significantly decreased in controls (p value = 0.03, OR = 0.6, 95% CI = 0.41-0.87). The frequency of CG genotype at position rs10754558 was also significantly higher in the controls compared with patients (p value = 0.03, OR = 0.5, 95% CI = 0.30-0.80).	These polymorphisms are suggested to be associated with the basal levels of IL‐1β and IL‐18.The G allele in rs10754558 was shown to enhance NLRP3 Mrna stability,leading to increased IL‐1 and IL‐18 secretion	30264444	Details
NLRP3	SNP	rs10754558	TaqMan method	MS	Disease risk	In this study, we found that NLRP3 rs3806265 C allele and CC genotype were significantly more frequent in the RRMS patients (p value = 0.03 OR = 1.66, 95% CI = 1.14-2.43) and p value = 0.04, OR = 3.26, 95% CI = 1.19-8.93, respectively), while the frequency of T allele significantly decreased in controls (p value = 0.03, OR = 0.6, 95% CI = 0.41-0.87). The frequency of CG genotype at position rs10754558 was also significantly higher in the controls compared with patients (p value = 0.03, OR = 0.5, 95% CI = 0.30-0.80).	These polymorphisms are suggested to be associated with the basal levels of IL‐1β and IL‐18.The G allele in rs10754558 was shown to enhance NLRP3 Mrna stability,leading to increased IL‐1 and IL‐18 secretion	30264444	Details
GSK3B	SNP	rs334558	Taqman methodology	MS	Disease risk	A statistically significant increased frequency of the rs334558 GG genotype was observed in patients as compared with controls.Stratifying MS patients according to the disease subtype, a statistically significant difference of rs334558 GG frequency was found between Relapsing Remitting (RR), but not Primary Progressive or Secondary MS, and controls.	Glycogen synthase kinase 3 beta gene (GSK3β) encodes for a serinethreonine kinase involved in numerous physiological responses by phosphorylating a variety of nuclear and cytoplasmic proteins, including tau. Abnormal hyperphosphorylation of tau is involved in the pathogenesis of some common neurodegenerative disorders, but it is also likely to play a role also in the pathogenesis of Multiple Sclerosis (MS).	21527318	Details
CXCL10	SNP	rs3921	Taqman methodology	MS	Disease risk	Therefore, the GGTT haplotype of the CXCL10 gene is not a susceptibility factor for the development of MS	CXCL10 (interferon-c-inducible protein-10) levels are increased in cerebrospinal fluid of multiple sclerosis (MS) patients with symptomatic attacks of inflammatory demyelination, supporting a role for this molecule in MS pathogenesis	17250724	Details
CXCL10	SNP	rs8878	Taqman methodology	MS	Disease risk	Therefore, the GGTT haplotype of the CXCL10 gene is not a susceptibility factor for the development of MS	CXCL10 (interferon-c-inducible protein-10) levels are increased in cerebrospinal fluid of multiple sclerosis (MS) patients with symptomatic attacks of inflammatory demyelination, supporting a role for this molecule in MS pathogenesis	17250724	Details
CXCL10	SNP	rs3921	Taqman methodology	MS	Treatment risk	but is probably to influence the course of MS, possibly contributing to slow down the progression of the disease.	CXCL10 (interferon-c-inducible protein-10) levels are increased in cerebrospinal fluid of multiple sclerosis (MS) patients with symptomatic attacks of inflammatory demyelination, supporting a role for this molecule in MS pathogenesis	17250724	Details
CXCL10	SNP	rs8878	Taqman methodology	MS	Treatment risk	but is probably to influence the course of MS, possibly contributing to slow down the progression of the disease.	CXCL10 (interferon-c-inducible protein-10) levels are increased in cerebrospinal fluid of multiple sclerosis (MS) patients with symptomatic attacks of inflammatory demyelination, supporting a role for this molecule in MS pathogenesis	17250724	Details
FCRL3	A functional promoter polymorphism	-169 T/C	TaqMan MGB	MS	Disease risk	An increased susceptibility associated to the -169 T allele was found when MS patients and controls were compared	FcRL3 has been shown to regulate gene expression and to play a role in several autoimmune diseases	17617473	Details
NR3C1	Gene polymorphisms	Haplotype 6 (TthIIII, ER2223EK, and 9beta-G	TaqMan PCR	MS	Disease risk	Haplotype 6 (TthIIII, ER2223EK, and 9beta-G) was associated with a more rapid disease progression	glucocorticoids might not be sufficiently able to restrain the immune system	19318444	Details
KIF1B	SNP	rs10492972	TaqMan PCR	MS	Disease risk	These results suggest that there is no effect in carrying the rs10492972 C variant on the risk of disease as well as on the rate of disability progression in a cohort of Italian patients with PPMS and patients with PRMS	KIF1B gene represents the first non-inflammatory gene with a putative role on axonal loss and neurodegeneration found to be associated with multiple sclerosis	20067515	Details
MTHFR	SNP	rs1801133	TaqMan PCR	MS	Disease risk	We found no association between polymorphisms of a folate-homocysteine-methionine-SAM metabolising gene enzyme and multiple sclerosis in a Polish population	5,10-methylenetetrahydrofolate reductase (MTHFR) is an essential enzyme involved in Hcy metabolism	31145465	Details
MTHFR	SNP	rs1801131	TaqMan PCR	MS	Disease risk	We found no association between polymorphisms of a folate-homocysteine-methionine-SAM metabolising gene enzyme and multiple sclerosis in a Polish population	5,10-methylenetetrahydrofolate reductase (MTHFR) is an essential enzyme involved in Hcy metabolism	31145465	Details
PLXNA3	SNP	rs5945430	TaqMan PCR	MS	Disease risk	Genotyping of 187 MS patients for rs5945430 confirmed the association of rs5945430G with increased disease severity in MS males	PLXNA3 rs5945430G is associated with increased disease severity in MS male patients	28536997	Details
STK11	SNP	rs9282860	TaqMan quantitative PCR assay	MS	Disease risk	The STK11-SNP has increased frequency in all female patients versus controls.	STK11 (serine-threonine-kinase 11) codes for liver kinase B1 (LKB1), a tumor suppressor gene. LKB1 functions upstream of at least 14 other protein kinases and, in that sense, is considered a master kinase with roles in numerous cellular functions. The wide array of functions regulated by LKB1 that have been implicated in the pathogenesis of MS suggest that alterations in LKB1 expression or activity may be a contributing factor to MS disease.	25694554	Details
IL21	SNP	rs13151961	TaqMan SNP Genotyping Assay	MS	Disease risk	IL21 has not been shown to be a major risk gene for MS.	Lack of genetic association	21736561	Details
IL21	SNP	rs6822844	TaqMan SNP Genotyping Assay	MS	Disease risk	IL22 has not been shown to be a major risk gene for MS.	Lack of genetic association	21736561	Details
IL21	SNP	rs925549	TaqMan SNP Genotyping Assay	MS	Disease risk	IL23 has not been shown to be a major risk gene for MS.	Lack of genetic association	21736561	Details
IL21	SNP	rs17879298	TaqMan SNP Genotyping Assay	MS	Disease risk	IL24 has not been shown to be a major risk gene for MS.	Lack of genetic association	21736561	Details
IL21	SNP	rs907715	TaqMan SNP Genotyping Assay	MS	Disease risk	IL25 has not been shown to be a major risk gene for MS.	Lack of genetic association	21736561	Details
IL21	SNP	rs4833837	TaqMan SNP Genotyping Assay	MS	Disease risk	IL26 has not been shown to be a major risk gene for MS.	Lack of genetic association	21736561	Details
IL21	SNP	rs13143866	TaqMan SNP Genotyping Assay	MS	Disease risk	IL27 has not been shown to be a major risk gene for MS.	Lack of genetic association	21736561	Details
IL21	SNP	rs17005929	TaqMan SNP Genotyping Assay	MS	Disease risk	IL28 has not been shown to be a major risk gene for MS.	Lack of genetic association	21736561	Details
IL21	SNP	rs17005931	TaqMan SNP Genotyping Assay	MS	Disease risk	IL29 has not been shown to be a major risk gene for MS.	Lack of genetic association	21736561	Details
IL21	SNP	rs12505138	TaqMan SNP Genotyping Assay	MS	Disease risk	IL30 has not been shown to be a major risk gene for MS.	Lack of genetic association	21736561	Details
IL21	SNP	rs4326027	TaqMan SNP Genotyping Assay	MS	Disease risk	IL31 has not been shown to be a major risk gene for MS.	Lack of genetic association	21736561	Details
IL21	SNP	rs6840978	TaqMan SNP Genotyping Assay	MS	Disease risk	IL32 has not been shown to be a major risk gene for MS.	Lack of genetic association	21736561	Details
VDR	SNP	rs2228570 (Fok1)	TaqMan SNP genotyping assays	MS	Disease risk	There was no evidence of disease association with the VDR SNP rs2228570 in the combined cohort.Similarly, there was no association in the case–control analysis, or over-transmission of either allele in the trio family dataset.	The minor allele (C) of rs731236 was found to be over-represented in MS in the combined case–control and trio family dataset. In the separate cohorts, there was a higher frequency of the minor allele in cases compared to healthy controls and a trend of over-transmission in the trio cohort.	21816760	Details
VDR	SNP	rs731236 (Taq1)	TaqMan SNP genotyping assays	MS	Disease risk	The minor allele (C) of rs731236 was found to be over-represented in MS in the combined case–control and trio family dataset. In the separate cohorts, there was a higher frequency of the minor allele in cases compared to healthy controls and a trend of over-transmission in the trio cohort.	The minor allele (C) of rs731236 was found to be over-represented in MS in the combined case–control and trio family dataset. In the separate cohorts, there was a higher frequency of the minor allele in cases compared to healthy controls and a trend of over-transmission in the trio cohort.	21816760	Details
SH2D2A	SNP	rs2768766	TaqMan technology	MS	Disease risk	the present study shows that the SH2D2A gene may contribute to susceptibility to MS.	N/A	18554728	Details
SH2D2A	SNP	rs909200	TaqMan technology	MS	Disease risk	the present study shows that the SH2D2A gene may contribute to susceptibility to MS.	N/A	18554728	Details
SH2D2A	SNP	rs926103	TaqMan technology	MS	Disease risk	the present study shows that the SH2D2A gene may contribute to susceptibility to MS.	N/A	18554728	Details
SH2D2A	SNP	rs1800600	TaqMan technology	MS	Disease risk	the present study shows that the SH2D2A gene may contribute to susceptibility to MS.	N/A	18554728	Details
SH2D2A	SNP	GA repeat polymorphism	TaqMan technology	MS	Disease risk	the present study shows that the SH2D2A gene may contribute to susceptibility to MS.	N/A	18554728	Details
SH2D2A	SNP	rs2768764	TaqMan technology	MS	Disease risk	the present study shows that the SH2D2A gene may contribute to susceptibility to MS.	N/A	18554728	Details
IL23R	SNP	rs7517847	TaqMan technology	CD、MS	Disease risk	rs7517847, did not show significant differences between patients and controls	increasing susceptibility to CD and MS	18368064	Details
IL23R	SNP	rs11209026	TaqMan technology	CD、MS	Disease risk	The analysis of IL23R polymorphisms showed susceptibility to both diseases marked by the presence of rs11209026_A	increasing susceptibility to CD and MS	18368064	Details
IL12B	SNP	rs6887695	TaqMan technology	CD、MS	Disease risk	There are no differences in IL12B genotypes conditioned by IL23R and vice versa	increasing susceptibility to CD and MS	18368064	Details
IL12B	SNP	rs3212227	TaqMan technology	CD、MS	Disease risk	There are no differences in IL12B genotypes conditioned by IL23R and vice versa	increasing susceptibility to CD and MS	18368064	Details
IL6	SNP	rs1818879	TaqMan Validate SNP Genotyping Assay	MS	Phenotypic risk	We found a significant association between rs1818879 and PC1.A significant association emerged between the SNP rs1818879 and radiological activity at diagnosis. In particular, the presence of the A allele was associated with a higher prevalence of gadolinium-enhancing lesions at the time of diagnosis.In rs1818879, A minor allele carriers significantly increasing CSF levels of both pro-inflammatory and anti-inflammatory cytokines have been observed.	Interleukin (IL)-6 represents one of the most important pro-inflammatory cytokines in the pathophysiology of MS.	35627281	Details
IL2RA	SNP	rs2104286	TaqMan、Affymetrix	MS	Disease risk	The most associated IL2RA SNP for MS susceptibility is rs2104286 located in intron 1 of IL2RA	The IL-2/IL-2RA(CD25) pathway plays an essential role in regulating immune responses	19119414	Details
CYP27B1	SNP	rs4646536	TaqMan、MALDI-TOF	MS	Disease risk	Three SNPs genotyped in the Swedish cohorts were associated with MS, rs4646536, rs10877012 and rs10877015	CYP27B1 is the most likely MS susceptibility candidate, given its importance in vitamin D3 activation and the important role of vitamin D3 in immunological functions	20648053	Details
CYP27B1	SNP	rs10877012	TaqMan、MALDI-TOF	MS	Disease risk	Three SNPs genotyped in the Swedish cohorts were associated with MS, rs4646536, rs10877012 and rs10877015	CYP27B1 is the most likely MS susceptibility candidate, given its importance in vitamin D3 activation and the important role of vitamin D3 in immunological functions	20648053	Details
CYP27B1	SNP	rs10877015	TaqMan、MALDI-TOF	MS	Disease risk	Three SNPs genotyped in the Swedish cohorts were associated with MS, rs4646536, rs10877012 and rs10877015	CYP27B1 is the most likely MS susceptibility candidate, given its importance in vitamin D3 activation and the important role of vitamin D3 in immunological functions	20648053	Details
CYP27B1	SNP	rs703842	TaqMan、MALDI-TOF	MS	Disease risk	We imputed rs703842 SNP and performed a joint analysis with the ANZgene results, reaching a significant association for rs703842	CYP27B1 is the most likely MS susceptibility candidate, given its importance in vitamin D3 activation and the important role of vitamin D3 in immunological functions	20648053	Details
HLA-C	SNP	rs2647040	TaqMan、PCR	MS	Disease risk	Two MHC class II SNPs, rs2647040 and rs3135021, were significant in the replication cohort and partially tagged DRB1*15 alleles.	Although the association of these two SNPs may be derived from their partial tagging of HLA-DRB1*15 alleles, it is still of interest to discuss other loci close to the SNPs. it is still possible that other alleles of DQB1 are associated independently of DRB1 with MS susceptibility in African Americans	20466734	Details
HLA-C	SNP	rs3135021	TaqMan、PCR	MS	Disease risk	Two MHC class II SNPs, rs2647040 and rs3135021, were significant in the replication cohort and partially tagged DRB1*15 alleles.	It is therefore possible that the association of rs3135021 with MS in African Americans may be through HLA-DPB1 rather than HLA-DRB1 alleles.	20466734	Details
TYK2	SNP	rs34536443	TaqMan、PCR	MS	Disease risk	we found that evidence for association was substantially increased for one of the 17 loci, rs34536443 from the tyrosine kinase 2 (TYK2) gene (P=2.7 x 10(-6), odds ratio=1.32 (1.17-1.47))	This single nucleotide polymorphism results in an amino acid substitution (proline to alanine) in the kinase domain of TYK2, which is predicted to influence the levels of phosphorylation and therefore activity of the protein and so is likely to have a functional role in multiple sclerosis.	19293837	Details
CCL22	SNP	rs223889	Taqman、PCR-RFLP	MS	Disease risk	No differencesin either allelic or genotypic frequency of the C/T SNP in CCL22 promoter were observed between cases and controls	N/A	17967467	Details
CCL22	SNP	rs4359426	Taqman、PCR-RFLP	MS	Disease risk	A trend towards a decreased allelic frequency of the A allele of the CCL22 C/A SNP as well as of the T allele of the CCL17 C/T SNP was found in patients compared with controls	the presence of theAThaplotype in chromosome 16 chemokine cluster is likely toconfer a decreased risk of developing MS	17967467	Details
CCL17	SNP	rs223828	Taqman、PCR-RFLP	MS	Disease risk	A trend towards a decreased allelic frequency of the A allele of the CCL22 C/A SNP as well as of the T allele of the CCL17 C/T SNP was found in patients compared with controls	the presence of theAThaplotype in chromosome 16 chemokine cluster is likely toconfer a decreased risk of developing MS	17967467	Details
GAS5	SNP	rs2067079	TaqMan、qPCR	MS	Disease risk	The rs2067079TT minor homozygote genotype was associated with an increased MS risk, while the rs1625579G minor allele was protective；rs1625579 showed an age-specific effect, while the rs2067079 affected the MS risk in gender- and age-specific manners	The long noncoding RNA GAS5 acts as a competing endogenous RNA for microRNA-137 and is involved in demyelination	32348112	Details
MIR137	SNP	rs1625579	TaqMan、qPCR	MS	Disease risk	The rs2067079TT minor homozygote genotype was associated with an increased MS risk, while the rs1625579G minor allele was protective；rs1625579 showed an age-specific effect, while the rs2067079 affected the MS risk in gender- and age-specific manners	The long noncoding RNA GAS5 acts as a competing endogenous RNA for microRNA-137 and is involved in demyelination	32348112	Details
CD40	SNP	rs1883832	TaqMan、qPCR	MS	Disease risk	In our study, both SNPs rs6074022 and rs1883832 were significantly associated with MS	We may speculate that the functional variant(s) is likely to be located in the upstream region of the gene CD40 and is in higher LD with rs6074022 than with rs1883832	23613777	Details
CD40	SNP	rs6074022	TaqMan、qPCR	MS	Disease risk	In our study, both SNPs rs6074022 and rs1883832 were significantly associated with MS	We may speculate that the functional variant(s) is likely to be located in the upstream region of the gene CD40 and is in higher LD with rs6074022 than with rs1883832	23613777	Details
CD40	SNP	rs1535045	TaqMan、qPCR	MS	Disease risk	Neither rs1535045 nor rs11086998 was associated with MS	N/A	23613777	Details
CD40	SNP	rs11086998	TaqMan、qPCR	MS	Disease risk	Neither rs1535045 nor rs11086998 was associated with MS	N/A	23613777	Details
IL7R	SNP	rs6897932	the Sequenom MassARRAY system	MS	Disease risk	This SNP was found to be associated with an increased risk of MS.	IL7R which was identified as one of the non-major Histocompatibility complex (non - MHC) genes is translated into a functional cell receptor for IL-7. IL7R plays an essential role in the maintenance, survival, homeostasis and proliferation of T cells, and may also have a key signalling influence through autoimmunity process.	32683075	Details
IL7R	SNP	rs13188960	the Sequenom MassARRAY system	MS	Disease risk	This SNP was found to be associated with an increased risk of MS.	IL7R which was identified as one of the non-major Histocompatibility complex (non - MHC) genes is translated into a functional cell receptor for IL-7. IL7R plays an essential role in the maintenance, survival, homeostasis and proliferation of T cells, and may also have a key signalling influence through autoimmunity process.	32683075	Details
LAG3	SNP	rs2365095	the Sequenom MassARRAY system	MS	Disease risk	This SNP was found to be associated with an increased risk of MS.	LAG3 which is another candidate gene involved in the MS susceptibility is encoded to 498-amino acid type I transmembrane protein (LAG3 or CD223) and mainly inhibit the activation of T cells, B cells, and natural killer (NK) cells.	32683075	Details
MERTK	SNP	rs867311	un-genotyped SNPs in the GWAS cohort	MS	Disease risk	In conclusion, this candidate gene study has identified an association of MS with 12 SNPs in the MERTK gene that replicated in two independent cohorts of MS cases and controls, an association that is particularly compelling given the previous studies implicating TAM receptor signalling in demyelination and autoimmunity. Further fine mapping studies will be required to determine the causal variant or variants	Susceptibility to MS is thought to involve a complex interplay of genetic and environmental factors, with the HLA-DRB1*1501-DQBI*602 (HLA-DR15) haplotype in the major histocompatibility complex (MHC) being the predominant genetic risk factor	21347448	Details
MERTK	SNP	rs12477716	un-genotyped SNPs in the GWAS cohort	MS	Disease risk	In conclusion, this candidate gene study has identified an association of MS with 12 SNPs in the MERTK gene that replicated in two independent cohorts of MS cases and controls, an association that is particularly compelling given the previous studies implicating TAM receptor signalling in demyelination and autoimmunity. Further fine mapping studies will be required to determine the causal variant or variants	Susceptibility to MS is thought to involve a complex interplay of genetic and environmental factors, with the HLA-DRB1*1501-DQBI*602 (HLA-DR15) haplotype in the major histocompatibility complex (MHC) being the predominant genetic risk factor	21347448	Details
MERTK	SNP	rs17835605	un-genotyped SNPs in the GWAS cohort	MS	Disease risk	In conclusion, this candidate gene study has identified an association of MS with 12 SNPs in the MERTK gene that replicated in two independent cohorts of MS cases and controls, an association that is particularly compelling given the previous studies implicating TAM receptor signalling in demyelination and autoimmunity. Further fine mapping studies will be required to determine the causal variant or variants	Susceptibility to MS is thought to involve a complex interplay of genetic and environmental factors, with the HLA-DRB1*1501-DQBI*602 (HLA-DR15) haplotype in the major histocompatibility complex (MHC) being the predominant genetic risk factor	21347448	Details
MERTK	SNP	rs4278932	un-genotyped SNPs in the GWAS cohort	MS	Disease risk	In conclusion, this candidate gene study has identified an association of MS with 12 SNPs in the MERTK gene that replicated in two independent cohorts of MS cases and controls, an association that is particularly compelling given the previous studies implicating TAM receptor signalling in demyelination and autoimmunity. Further fine mapping studies will be required to determine the causal variant or variants	Susceptibility to MS is thought to involve a complex interplay of genetic and environmental factors, with the HLA-DRB1*1501-DQBI*602 (HLA-DR15) haplotype in the major histocompatibility complex (MHC) being the predominant genetic risk factor	21347448	Details
MERTK	SNP	rs4528767	un-genotyped SNPs in the GWAS cohort	MS	Disease risk	In conclusion, this candidate gene study has identified an association of MS with 12 SNPs in the MERTK gene that replicated in two independent cohorts of MS cases and controls, an association that is particularly compelling given the previous studies implicating TAM receptor signalling in demyelination and autoimmunity. Further fine mapping studies will be required to determine the causal variant or variants	Susceptibility to MS is thought to involve a complex interplay of genetic and environmental factors, with the HLA-DRB1*1501-DQBI*602 (HLA-DR15) haplotype in the major histocompatibility complex (MHC) being the predominant genetic risk factor	21347448	Details
MERTK	SNP	rs17174870	un-genotyped SNPs in the GWAS cohort	MS	Disease risk	In conclusion, this candidate gene study has identified an association of MS with 12 SNPs in the MERTK gene that replicated in two independent cohorts of MS cases and controls, an association that is particularly compelling given the previous studies implicating TAM receptor signalling in demyelination and autoimmunity. Further fine mapping studies will be required to determine the causal variant or variants	Susceptibility to MS is thought to involve a complex interplay of genetic and environmental factors, with the HLA-DRB1*1501-DQBI*602 (HLA-DR15) haplotype in the major histocompatibility complex (MHC) being the predominant genetic risk factor	21347448	Details
MERTK	SNP	rs1516629	un-genotyped SNPs in the GWAS cohort	MS	Disease risk	In conclusion, this candidate gene study has identified an association of MS with 12 SNPs in the MERTK gene that replicated in two independent cohorts of MS cases and controls, an association that is particularly compelling given the previous studies implicating TAM receptor signalling in demyelination and autoimmunity. Further fine mapping studies will be required to determine the causal variant or variants	Susceptibility to MS is thought to involve a complex interplay of genetic and environmental factors, with the HLA-DRB1*1501-DQBI*602 (HLA-DR15) haplotype in the major histocompatibility complex (MHC) being the predominant genetic risk factor	21347448	Details
Ankrd55	SNP	rs6859219	WB;ELISA	EAE	Disease risk	Brain samples from EAE mice also showed a significant increase in ANKRD55	N/A	27183579	Details
VAV1	SNP	rs2546133-rs2617822	We used TAGGER in Haploview version 3.32 (49) and ENTROPY as implemented in Marker software for identifying tSNPs	MS	Disease risk	VAV1 plays a central role in controlling central nervous system immunemediated disease and proinflammatory cytokine production critical for disease pathogenesis.	N/A	20368159	Details
HLA-DPB1	N/A	HLA-DPB1*0501	Westren	MS	Disease risk	The marked differences in the clinical and MRI findings as well as in the immunogenetic backgrounds between the opticospinal multiple sclerosis and Western-type multiple sclerosis together suggest that HLA-DPB1*0501-associated opticospinal multiple sclerosis is a distinct subtype of multiple sclerosis.	N/A	10468508	Details