We next examined the relative ability of the three datasets to detect eQTLs from regions nominated in GWAS. We abstracted SNPs associated with human traits based on the NHGRI catalog of GWA, yielding1366 loci. Of these, 783 SNPs passed the criteria of having a replicated association with traits or diseases and being within 0.5 MB of the chromosomal position of a probe for gene expression. We chose the threshold of 0.5 MB based on previous data (Gibbs et al., 2010) where we saw the average distance between a SNP and significant eQTL was 121 Kb and > 90% of significant eQTLs were detected within 0.5 MB.
