In total, 47.5% of GWAS SNPs fall within gene bodies (fig. SIB); however, only 10.9% of intronic GWAS SNPs within DHSs are in strong LD (r2≥0.8) with a coding SNP, indicating that the vast majority of noncoding genie variants are not simply tagging coding sequence. Analogously, only 16.3% of GWAS variants within coding sequences are in strong LD with variants in DHSs. We noted that SNPs on widely used genotyping arrays (e.g., Affymetrix) were modestly enriched within DHSs (fig. S2), possibly due to selection of SNPs with robust experimental performance in genotyping assays. However, we found no evidence for sequence composition bias (table S3).
