User's Guide
Best experienced using the browsers Chrome Firefox Safari or IE version (9,10,11)
Get an overview of LincSNP 3.0 from the Home page. The Home page is displayed in Figure 1-1:
Figure 1-1:
1. Main functions of the database are provided in menu bar form (boxed in red).
2. The brief introduction of LincSNP 3.0.
3. A quick search for experimentally verified data linked to 'Variant Confirm'.
4. The number of regulatory relationships among diverse variants, lncRNAs and regulatory elements (different color represent different regulatory relationship).
5. The data growth of LincSNP 3.0 compared to LincSNP 2.0.
6. New features of LincSNP 3.0 compared to LincSNP 2.0.
7. A link to old version LincSNP 1.0 and LincSNP 2.0.
Figure 1-1
How to search and browse the information in Variant Confirm?
Variant Confirm stores all experimentally supported variant-lncRNA-disease associations manually collected from the published literature. The search and browse way for experimentally supported variant-lncRNA-disease associations is displayed in Figure 2-1.
1. Input your interested disease or trait, such as lung cancer or type 2 diabetes.
2. Input your interested lncRNA name, such as ANRIL or CASC8.
3. Input your interested SNP or copy number variation ID, such as rs10120688 or rs10505477.
4. Select your interested association, including circulating, survival, ceRNA, methylation, enhancer and drug.
5. After step 1, 2 or 3, you will get the result page with the target entries.
6. Click to download data, including copy detail information, excel file format, csv file format, and pdf file format.
7. Users can input keywords from any column to filter the results.
8. You could also directly click your interested association for detail information.
Figure 2-1
How to read the detail information of the entry in Variant Confirm?
Detailed information of a specific association is displayed in Figure 2-2:
1. The basic information of lncRNA and variant, including RNA name, variant type, variant ID and species.
2. The additional information including circulating, survival, ceRNA, methylation and enhancer and drug.
3. The experimental and publication information, including disease/trait, target gene, tissue, experiment, fuction, PMID, etc.
4. The external links for lncRNA and disease.
Figure 2-2
How to search for information by the interested variant in Functional Variant ?
The search way by diverse variants including SNP, LD SNP, somatic mutation and RNA editing.
For SNP Search, the search direction and brief result interpretation are displayed in Figure 3-1:
1. Input your interested disease or trait, such as colorectal cancer or heart.
2. Input your interested SNP ID, such as rs2476 or rs464274.
3. Select your interested region, including chromosome, start and end.
4. Select lncRNA or circRNA.
5. Select your interested RNA or regulatory element, including RNA region, TFBS, enhancer, DHS, footprints, TAD, chromatin accessibility and meth-QTL.
6. After above steps, you will get the brief information with the target entries.
Figure 3-1
For LD SNP Search, the search direction and brief result interpretation are displayed in Figure 3-2:
1. Input your interested SNP ID, such as rs9662595 or rs2222371.
2. Select your interested region, including chromosome, start and end.
3. Select lncRNA or circRNA.
4. Select your interested RNA or regulatory element, including RNA region, TFBS, enhancer, DHS, footprints, TAD and chromatin accessibility.
5. After above steps, you will get the brief information with the target entries.
Figure 3-2
For Somatic Mutation search, the search direction and brief result interpretation are displayed in Figure 3-3:
1. Input your interested cosmic mutation ID, such as COSV50351041 or COSN16136502.
2. Select your interested region, including chromosome, start and end.
3. Select lncRNA or circRNA.
4. Select your interested RNA or regulatory element, including RNA region, TFBS, enhancer, DHS, footprints, TAD and chromatin accessibility.
5. After above steps, you will get the brief information with the target entries.
Figure 3-3
For RNA Editing Search, the search direction and brief result interpretation are displayed in Figure 3-4:
1. Select your interested tissue, such as breast or heart.
2. Select your interested region, including chromosome, start and end.
3. Select lncRNA or circRNA.
4. Select your interested RNA or regulatory element, including RNA region, TFBS, enhancer, DHS, footprints, TAD and chromatin accessibility.
5. After above steps, you will get the brief information with the target entries.
Figure 3-4
How to browse the result information of the interested variant in Disease Variant ?
LincSNP 3.0 results are organized in a data table, with a single association record on each line that contains variant detail, SNP ID, population, gene, allele frequency, PubMed ID, regulatory element detail, regulatory name, RNA detail, RNA ID.
The SNP detailed result page of interested entries is displayed in Figure 3-5.
1. Select your interested regulatory elements, including RNA region, TFBS, enhancer, DHS, footprints, TAD, chromatin accessibility and meth-QTL.
2. Click to download data, including copy detail information, excel file format, csv file format, and pdf file format.
3. Users can input keywords from any column to filter the results.
4. Click to get detail information of variant, including SNP, genome position, disease/trait and population.
5. Click to get detail information of regulatory element.
6. Click to get detail information of RNA, including name and genome position of lncRNA or circRNA.
Figure 3-5
The LD SNP detailed result page of interested entries is displayed in Figure 3-6.
1. Select your interested regulatory elements, including RNA region, TFBS, enhancer, DHS, footprints, TAD and chromatin accessibility.
2. Click to download data, including copy detail information, excel file format, csv file format, and pdf file format.
3. Users can input keywords from any column to filter the results.
4. Click to get detail information of RNA, including name and genome position of lncRNA or circRNA.
Figure 3-6
The Somatic Mutation detailed result page of interested entries is displayed in Figure 3-7.
1. Select your interested regulatory elements, including RNA region, TFBS, enhancer, DHS, footprints, TAD and chromatin accessibility.
2. Click to download data, including copy detail information, excel file format, csv file format, and pdf file format.
3. Users can input keywords from any column to filter the results.
4. Click to get detail information of RNA, including name and genome position of lncRNA or circRNA.
Figure 3-7
The RNA Editing detailed result page of interested entries is displayed in Figure 3-8.
1. Select your interested regulatory elements, including RNA region, TFBS, enhancer, DHS, footprints, TAD and chromatin accessibility.
2. Click to download data, including copy detail information, excel file format, csv file format, and pdf file format.
3. Users can input keywords from any column to filter the results.
4. Click to get detail information of RNA, including name and genome position of lncRNA or circRNA.
Figure 3-8
How to search for functional variant (GWAS SNPs, SNPs that in LD with the GWAS SNPs, Somatic Mutation and RNA Editing) centered on lncRNA in RNA-centric?
For SNP of lncRNA, the RNA-centric Search direction and result interpretation are displayed in Figure 4-1:
1. Input your interested lncRNA ID or name, such as ENSG00000267107.7, ENSG00000267107, NONHSAG073520.1, NONHSAG073520 or PCAT19.
2. Click the SNP of variant type.
3. Select your interested RNA or regulatory element, including RNA region, TFBS, enhancer, DHS, footprints, TAD, chromatin accessibility and meth-QTL.
4. Click the Search button to turn to results page.
5. Click to download data, including copy detail information, excel file format, csv file format, and pdf file format.
6. Users can input keywords from any column to filter the results.
7. Click to get detail information of variant, including SNP, genome position, disease/trait and population.
8. Click to get detail information of regulatory element.
9. Click to get detail information of lncRNA, including gene ID, gene name, gene position, transcript ID, transcript name, transcript position, gene type and transcript type.
Figure 4-1
For LD SNP of lncRNA, the RNA-centric Search direction and result interpretation are displayed in Figure 4-2:
1. Input your interested lncRNA ID or name, such as ENSG00000267107.7, ENSG00000267107, NONHSAG073520.1, NONHSAG073520 or PCAT19.
2. Click the LD SNP of variant type.
3. Select your interested RNA or regulatory element, including RNA region, TFBS, enhancer, DHS, footprints, TAD and chromatin accessibility.
4. Click the Search button to turn to results page.
5. Click to download data, including copy detail information, excel file format, csv file format, and pdf file format.
6. Users can input keywords from any column to filter the results.
7. Click to get detail information of lncRNA, including gene ID, gene name, gene position, transcript ID, transcript name, transcript position, gene type and transcript type.
Figure 4-2
For Somatic Mutation of lncRNA, the RNA-centric Search direction and result interpretation are displayed in Figure 4-3:
1. Input your interested lncRNA ID or name, such as ENSG00000253320.6, ENSG00000253320, NONHSAG061490.2, NONHSAG061490 or AZIN1-AS1.
2. Click the Somatic Mutation of variant type.
3. Select your interested RNA or regulatory element, including RNA region, TFBS, enhancer, DHS, footprints, TAD and chromatin accessibility.
4. Click the Search button to turn to results page.
5. Click to download data, including copy detail information, excel file format, csv file format, and pdf file format.
6. Users can input keywords from any column to filter the results.
7. Click to get detail information of lncRNA, including gene ID, gene name, gene position, transcript ID, transcript name, transcript position, gene type and transcript type.
Figure 4-3
For RNA Editing of lncRNA, the RNA-centric Search direction and result interpretation are displayed in Figure 4-4:
1. Input your interested lncRNA ID or name, such as ENSG00000267107.7, ENSG00000267107, NONHSAG073520.1, NONHSAG073520 or PCAT19.
2. Click the RNA Editing of variant type.
3. Select your interested RNA or regulatory element, including RNA region, TFBS, enhancer, DHS, footprints, TAD and chromatin accessibility.
4. Click the Search button to turn to results page.
5. Click to download data, including copy detail information, excel file format, csv file format, and pdf file format.
6. Users can input keywords from any column to filter the results.
7. Click to get detail information of lncRNA, including gene ID, gene name, gene position, transcript ID, transcript name, transcript position, gene type and transcript type.
Figure 4-4
How to search for functional variant (GWAS SNPs, SNPs that in LD with the GWAS SNPs, Somatic Mutation and RNA Editing) centered on circRNA in RNA-centric?
For SNP of circRNA, the RNA-centric Search direction and result interpretation are displayed in Figure 4-5:
1. Input the overlapping coding gene ID or name of circRNA, such as ENSG00000134250 or NOTCH2.
2. Select chromosome and input the region location, including chromosome, start and end.
3. Click the SNP of variant type.
4. Select your interested RNA or regulatory element, including RNA region, TFBS, enhancer, DHS, footprints, TAD, chromatin accessibility.
5. Click the Search button to turn to results page.
6. Click to download data, including copy detail information, excel file format, csv file format, and pdf file format.
7. Users can input keywords from any column to filter the results.
8. Click to get detail information of variant, including SNP, genome position, disease/trait and population.
9. Click to get detail information of regulatory element.
10. Click to get detail information of circRNA, including circRNA name and gene position.
Figure 4-5
For LD SNP of circRNA, the RNA-centric Search direction and result interpretation are displayed in Figure 4-6:
1. Input the overlapping coding gene ID or name of circRNA, such as ENSG00000134250 or NOTCH2.
2. Select chromosome and input the region location, including chromosome, start and end.
3. Click the LD SNP of variant type.
4. Select your interested RNA or regulatory element, including RNA region, TFBS, enhancer, DHS, footprints, TAD, chromatin accessibility.
5. Click the Search button to turn to results page.
6. Click to download data, including copy detail information, excel file format, csv file format, and pdf file format.
7. Users can input keywords from any column to filter the results.
Figure 4-6
For Somatic Mutation of circRNA, the RNA-centric Search direction and result interpretation are displayed in Figure 4-7:
1. Input the overlapping coding gene ID or name of circRNA, such as ENSG00000134250 or NOTCH2.
2. Select chromosome and input the region location, including chromosome, start and end.
3. Click the Somatic Mutation of variant type.
4. Select your interested RNA or regulatory element, including RNA region, TFBS, enhancer, DHS, footprints, TAD, chromatin accessibility.
5. Click the Search button to turn to results page.
6. Click to download data, including copy detail information, excel file format, csv file format, and pdf file format.
7. Users can input keywords from any column to filter the results.
Figure 4-7
For RNA Editing of circRNA, the RNA-centric Search direction and result interpretation are displayed in Figure 4-8:
1. Input the overlapping coding gene ID or name of circRNA, such as ENSG00000134250 or NOTCH2.
2. Select chromosome and input the region location, including chromosome, start and end.
3. Click the RNA Editing of variant type.
4. Select your interested RNA or regulatory element, including RNA region, TFBS, enhancer, DHS, footprints, TAD, chromatin accessibility.
5. Click the Search button to turn to results page.
6. Click to download data, including copy detail information, excel file format, csv file format, and pdf file format.
7. Users can input keywords from any column to filter the results.
Figure 4-8
How to browse your interested variants, lncRNAs or circRNAs and their associated elements in Genome browser?
The browse direction is displayed in figure 5-1:
1. Input the genomic position of your interested variants, lncRNAs/cirRNAs, RNA associated elements and click search to get transcript information in Genome Browser.
2. Select interested tracks, including variant, non-coding RNA and element.
3. Users can check the structure and basic information of the transcript, variant or regulate-element in Genome Browser, including name, position, length, gene ID, gene name, gene type, etc.
4. Click the left or right button, enter the chromosome area, or directly drag the window to slide the window, or click the zoom lens to adjust the window size.
5. Click to input your own genome to browse, such as a FASTA file (.fa) or indexed FASTA (.fa and .fai).
6. Click to input a track file or add track to Browser, for example, users can add any combination of data files and URLs, and JBrowse will automatically suggest tracks to display their contents.
7. Click to set highlight regions in genome, for example, users can input chr6:111741308..111874401 to highlight the location.
Figure 5-1
How to use Variant Mapper get related RNA and regulatory element about specific variants?
Variant Mapper allow users input interested variants and the mapper tool could map it on corresponding RNAs and regulatory elements. An example about operational process and interpretation of results are displayed in Figure 6-1.
1. Input your interested variants, including chromosome, start and end, such as chr7 30174530 30175031 (split by tab)
2. Select lncRNA or circRNA.
3. Select interested RNA or regulatory elements, including RNA region, TFBS, enhancer, DHS, footprints, TAD and chromatin accessibility.
4. You will get a result table for your interested variant.
5. Click to select your interested regulatory elements to display.
6. Click to download data, including copy detail information, excel file format, csv file format, and pdf file format.
7. Users can input keywords from any column to filter the results.
8. Click to get detail information of RNA, including name and genome position of lncRNA or circRNA.
Figure 6-1
How to use Circos Plotter get a specific disease related circos plot?
Circos Plotter is a tool which could provide a circos plot for a specific disease or tissue. An example of Microalbuminuria related circos-plot and result interpretation are displayed in Figure 7-1.
1. Input your interested disease or trait, such as Rheumatoid arthritis or Type 2 diabetes.
2. Click to select associated RNA (lncRNA or circRNA).
3. Click to select RNA and regulate element, including RNA region, TFBS, enhancer, DHS, footprints, TAD and chromatin accessibility.
4. Click the search button and you will get circos plot in the result page.
5. Color bar to divide different RNAs and regulatory elements.
6. Resting the mouse on the scatter, you can get the specific information of the point, including chromosome, position, value and genotype.
7. Resting the mouse on the chromosome, you can get specific information about the area, including chromosome, start and end.
8. Click to download the circos plot.
Figure 7-1
How to get Functional Annotation results of the interested variants?
Functional Annotation is a tool which could provide functional terms related with the annotated regions that overlap with the interested variants. An example about operational process and interpretation of results are displayed in Figure 8-1.
1. Input genomic position of your interested variants, including chromosome, start and end.
2. Click to select associated RNA (lncRNA or circRNA).
3. Click to select RNA and regulate element, including RNA region, TFBS, enhancer, DHS, footprints, TAD and chromatin accessibility.
4. Click the search button and you will get functional annotation results in the result page.
5. A summary graph page of the annotated regions, including number of associated genes per region, binned by orientation and distance to TSS and binned by absolute distance to TSS.
6. The resulting functional terms related with the input variants, including GO biological process, cellular component, molecular function, etc.
Figure 8-1