We tested the enrichment of SNPs from individual Genome-wide Association Studies (GWAS) for the gapped peak call sets based on histone marks H3K4me1, H3K4me3, H3K36me3, H3K9me3, H3K27me3, H3K9ac, and H3K27ac as well as the DNase peak call set based on MACS2 in each reference epigenome where available. The SNPs used were curated into the NHGRI GWAS catalog74 and obtained through the UCSC Table Browser118 on September 12, 2014. We restricted the enrichment analysis to chr1-22 and chrX. We defined a study to be a unique combination of annotated trait and pubMedID. To reduce dependencies between pairs of SNPs assigned to the same study, we pruned SNPs such that no two SNPs were within 1MB of each other on the same chromosome. The pruning procedure considered each SNP in ranked order of p-value with the the most significant coming first, and we retained a SNP if there was no already retained SNP on the same chromosome within 1MB. We computed hypergeometric p-values for the enrichment of each pruned set of SNPs overlapping peak calls against the pruned GWAS catalog as the
