100 simulations conditioned on MAF for these 10,000 SNPs was 117–178. No such enrichment was observed for other ways of prioritizing SNPs for function, including missense SNPs (the proportion of non-synonymous SNPs with Crohn's association p<0.01 was 0.0152), coding-synonymous substitutions (0.0253), or intronic SNPs (0.0158). We then differentiated the SNPs as “cis-regulators” (these are eQTLs for genes that are within 4 Mb) and “trans-regulators” (these are eQTLs for genes that are more than 4 Mb away or on a different chromosome). The Bonferroni adjustment of significance was different for the cis- and trans-regulators (see Materials and Methods). The enrichment was preserved in the SNPs classified as cis-regulators but was not evident in the SNPs classified as trans-regulators, suggesting that cis-regulatory effects were more likely to be present among the Crohn's associated SNPs.
