To investigate whether the eQTL enrichment we observe in the NHGRI variants is driven by linkage disequilibrium (LD), an LD-pruned SNP set was generated from the NHGRI list using r2<0.3. We then performed an eQTL enrichment analysis on this set, using a permutation procedure on 100 randomized sets of SNPs that reflect the LD-pruned set's MAF distribution. To show that the eQTL enrichment is not dependent on the particular LD-pruned set chosen, we generated 100 such LD-pruned sets on each of which 100 simulations were performed, as just described (Figure S3).
