Genevar Quick Start: cis-eQTL – SNP

Snapshot

In this example

• Observed SNP-gene associations in a 2-Mb region surrounding rs13277113 SNP in eight HapMap3 populations
• Significant genes within the chromosome region are listed below
• Dotted line represents the 0.001 p-value threshold
• Results can be saved as a PNG diagram or exported as a tab-delimited list
• External links to three major genome browsers

Step-by-Step Guide

1. 

   

   Click on "cis-eQTL – SNP".
2. Select a group of interest (e.g. HapMap3).
3. 

   

   Available expression-genotype pairs will be listed here.
4. 

   

   Choose reference source (e.g. Ensembl).
5. Type in SNPs here (e.g. rs13277113).
6. Select populations of interest.
7. Set parameters (e.g. Spearman's rho, 1 Mb, p < 0.001).
8. Submit to get transcript lists.
9. 

   

   A new tree node containing matched trascripts will be added here. Click on this node.
10. 

    

    Probes within this 2-Mb region will be listed below; significant ones are clicked as "chosen".
11. 

    

    Set parameters (e.g. Spearman's rho, 10,000 permutations).
12. Submit to get SNP-probe association plots.
13. 

    

    New tree nodes containing association plots for each transcript will be added here. Click on one of them.
    

    

    SNP-probe association plots.

Gene Start Sites

• 

  

  Sophisticated SQL query fetches both PDE4B (+) and GPR177 (-) even though their gene starts are outside the 2-Mb region.