Genevar Quick Start: eQTL – SNP-Gene

Snapshot

In this example

• SNP-probe association plots in eight HapMap3 populations
• Spearman's rho, nominal p-value and permutation p-value are shown above each plot
• Information of SNP-probe pairs will be displayed in a tip text when hovering the cursor over individual of interest

Step-by-Step Guide

1. 

   

   Click on "eQTL – SNP-Gene".
2. Select a dataset of interest (e.g. HapMap3).
3. Choose reference source (e.g. Ensembl).
4. Type in gene symbol of interest (e.g. IRF5).
5. Match entire word (optional)?
6. Submit and search from the selected platform and source.
7. 

   

   Query results will be listed here.
8. Select genes of interest.
9. Submit and find matched transcripts.
10. 

    

    A new tree node containing matched trascripts will be added here. Click on this node.
11. 

    

    Select populations of interest.
12. Select probes of interest.
13. Type in SNP IDs here (e.g. rs12155080).
14. Set parameters (e.g. Spearman's rho, 10,000 permutations).
15. Submit to get SNP-probe association plots.
16. 

    

    16. A new tree node containing association plots will be added here. Click on this node.
    

    

    SNP-probe association plots.