total variants) with a similar distance to the nearest gene (± 11,655 bp), number of variants in LD (±8 variants), and minor allele frequency. Using these pools, we created 10,000 sets of control variants for each of the 97 loci and identified variants in LD (r2 > 0.7) and within 1 Mb. For each SNP set, we calculated the number of loci with at least one variant located in a regulatory region under the assumption that one regulatory variant is responsible for each association signal. We estimated the P value assuming a sum of binomial distributions to represent the number of index SNPs (or their LD proxies; r2 > 0.7) that overlap a regulatory data set compared to the expectation observed in the 500 matched control sets. Data sets were considered significantly enriched if the P value was below a Bonferroni-corrected threshold of 1.2 × 10−3, adjusting for 41 tests.
