Genevar Quick Start: cis-eQTL – Gene

Snapshot

In this example:

  • Observed eQTLs in a 2-Mb window around the GBP3 locus in HapMap3 CHB
  • Significant SNPs within the chromosome region are listed below
  • Dotted line represents the 0.001 p-value threshold
  • Information of SNPs will be displayed in a tip text when hovering the cursor over the SNP of interest
  • 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 – 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. GBP3).
  5. Match entire word (optional)?
  6. Submit and search from the selected dataset and reference.
  7. Query results will be listed here.
  8. Select genes of interest.
  9. Submit to find matched transcripts.
  10. A new tree node containing matched trascripts for each gene will be added here. Click on this node.
  11. Select populations of interest.
  12. Select probes of interest.
  13. Set parameters (e.g. Spearman's rho, 1 Mb, p < 0.001).
  14. Submit to get mapping results.
  15. New tree nodes containing mapping results for each populaiton will be added here. Click on one of them.
    All eQTLs within this 2-Mb region will be plotted on a chromosome view; only significant SNPs are listed below.

Genevar - Hints on exporting diagrams, zooming in/back, and details of eQTLs

Exporting Diagrams

Right-click on the diagram and choose Save as.

Right-click on the diagram and choose Save as.

zoom

Zoom in

Left-click and drag the mouse from top-left to buttom-center in order to draw a rectangle.

Left-click and drag the mouse from top-left to buttom-center in order to draw a rectangle.

zoom

Then release the mouse button.

Then release the mouse button.

zoom

Zoom back

Press the mouse button and move backwards before release it.

Press the mouse button and move backwards before release it.

zoom

Details of eQTLs

It will be displayed in a tip text when hovering the mouse pointer over the eQTL of interest.

It will be displayed in a tip text when hovering the mouse pointer over the eQTL of interest.

zoom

* quick link - http://q.sanger.ac.uk/d3djddjp