Because some GWAS report associations for SNPs that were interrogated through imputation rather than direct genotyping, we repeated the analysis described above except that we used the entire set of HapMap SNPs to generate the 1000 randomized SNP sets with MAF matched to catalog SNPs, rather than only the SNPs included on high throughput GWAS platforms. Results of these studies show an even more significant enrichment of eQTLs among catalog SNPs (Figure S2). Thus, we focus in this paper on the more conservative results obtained using the simulations generated from SNPs on high-throughput GWAS platforms.
