Genome-wide Association Study Results and Enrichment Analyses
All SNPs published by 02/01/2012 were downloaded from the catalog of GWASs maintained by the NHGRI and filtered for 5,570 common variants (MAF > 5%) in the YRI samples examined. For overlap with eQTLs and pQTLs, we considered all SNPs in linkage disequilibrium (LD) (R2 > 80%) with the complex-trait-associated SNPs and filtered for common variants (MAF > 5%) in the YRI samples examined. To determine the enrichment for SNPs associated with each complex trait to be eQTLs or pQTLs, we focused on only the 7,222 primary-trait-associated SNPs before LD imputation to correct for LD-driven inflation of enrichment results. We then generated 1,000 randomized SNP sets each of size 7,222 and matched on MAF distribution by proportions in discrete 5% MAF bins. For each set, we determined the number of eQTLs and pQTLs at p < 10−4 for traits with at least three observed expression QTL overlaps and derived an empirical p value by comparing the proportion of random simulations in which the number of random overlaps exceeded the observed overlap.