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.
* quick link - http://q.sanger.ac.uk/nmk5uf8s