For robust enhancers (center +/− 200 bp), promoters (unique locations of RefSeq protein-coding gene transcript TSSs +/− 200 bp), exons (unique locations of RefSeq protein-coding gene transcript inner exons), and random regions (described above), we calculated the number of overlapping and non-overlapping GWAS SNPs associated with each disease/trait in the extended GWAS catalog. Non-associated SNPs were extracted from the NCBI single nucleotide polymorphism database (dbSNP, build 135). For each genomic feature and disease/trait with an odds ratio > 1, we tested whether the observed overlap was significantly greater than expected (Fisher's exact test P < 0.01). Only diseases/traits with more than three SNPs overlapping were tested. The same analysis was repeated for each set of significantly expressed enhancers associated with each facet. For ease of visualization and interpretation, only odds ratios for which the filtering criteria on both significance and overlap number were met are shown. Lists of enhancer-overlapped GWAS SNPs are in S16.
