The integration of eQTL results with GWAS has been proposed as a way to move toward biological and mechanistic understanding of complex trait etiology [32], [33], and is already achieving success [e.g.,34]. It has also recently been demonstrated that genome-wide association signals are enriched for eQTLs [5], [6], [7]. We compared our cis-eQTL results to the National Institute of Health's catalog of genome-wide association studies [35], [36], and found that of 4,772 GWAS SNPs representing 475 traits (available as of August 4, 2011), 62 SNPs were also the most-significant SNP of a cis-eQTL in at least one population (0.01 permutation threshold, ‘REDUCED’ analysis). These 62 SNPs associate with expression of 57 Ensembl genes, and 51 traits, including Alcohol dependence, Crohn's disease, Coronary Heart Disease, HDL cholesterol, Prostate Cancer, Trigylcerides, and many others (Table S7). The majority of GWAS studies have been performed in populations of Caucasian ancestry, however the overlap of GWAS SNPs to the strongest-associated cis-eQTLs did not reflect this; instead all populations were represented (CEU: N = 14 SNPs, CHB: N = 10, GIH: N = 9, JPT:
