We divided the SNPs into groups of 10,000 (in the order of their eQTL scores) and counted the number of SNPs in each group with p<0.01 for association with Crohn's disease - see Figure 2 (there are just over 123K SNPs with scores larger than 0). The first 10,000 SNPs (ranked according to eQTL function score) include 357 with Crohn's association p-values smaller than 0.01. We simulated sets of SNPs with allele frequencies matching the top 10,000 and, in 100 simulations, the range of this statistic (number of p-values smaller than 0.01) is 117–178 which is far less than the observed number.
