Genevar Quick Start: cis-eQTL – Gene

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

Click on "cis-eQTL – Gene".
Select a dataset of interest (e.g. HapMap3).
Choose reference source (e.g. Ensembl).
Type in gene symbol of interest (e.g. GBP3).
Match entire word (optional)?
Submit and search from the selected dataset and reference.
Query results will be listed here.
Select genes of interest.
Submit to find matched transcripts.
A new tree node containing matched trascripts for each gene will be added here. Click on this node.
Select populations of interest.
Select probes of interest.
Set parameters (e.g. Spearman's rho, 1 Mb, p < 0.001).
Submit to get mapping results.
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.