Understanding the functional impact of genetic markers of susceptibility to disease is of central importance in determining mechanisms of pathogenesis1,50. Whilst disease susceptibility loci can be associated with differential gene expression, just as with eQTL in general, this effect may be cell-specific. It is also probable many disease-associated eQTL only manifest under physiological conditions of mixed cell populations permitting appropriate cellular interactions and antigen exposure. We hypothesized that analysis of primary B-cells and monocytes freshly isolated from peripheral blood may identify such eQTL with the attractive promise of delineating functional activity to the innate or adaptive arms of the immune response. We investigated eQTLs involving SNP markers identified as a disease risk alleles at genome-wide significance (p < 5×10−8) for 548 common traits listed in the Catalog of Published Genome-Wide Association Studies (10th September 2011). We find that 49.4% of traits (17.3% of reported GWAS SNPs) are associated with one or more significant cis-eQTL based on the listed GWAS markers or identified proxy SNPs from the 1000 Genomes Project (CEU cohort, r2 > 0.8). A complete integrated dataset indexed by
