We downloaded the entire set of GWAS-suggestive and/or significant variants (by rs number) for thousands of traits from the NHGRI GWAS catalog31. We computed the odds ratio and corresponding p-value for enrichment for GWAS-associated variants by determining which variants were meQTLs and GWAS-associated, meQTLs only, GWAS-associated only, and neither, among those 7,426,085 SNPs considered in our dataset. For the PGC2 analysis, we obtained LD-clumped regions from the discovery dataset from the May 2013 freeze in the Ricopili tool (“PGC_SCZ52_may13”) which contains marginally significant regions (down to p-value < 10−4) and LD-proxies to each index SNP. We matched these SNPs to our data by chromosome and position, and determined which had a meQTL in our dataset.
