In order to understand the practical utility of our observation that trait-associated SNPs are more likely to be eQTLs, we examined in more detail results summaries from the Wellcome Trust Case Control Consortium (WTCCC) GWAS [11], using the data on Crohn's disease as a primary example application. If SNPs associated with Crohn's disease are no more likely than non-associated SNPs to be eQTLs, we would expect the proportion of SNPs associated with Crohn's disease at p<.01 in bins defined according to eQTL function score (see Materials and Methods for definition of eQTL function score) to be constant (the overall proportion of Crohn's p-values smaller than .01 is .0152). Instead, as illustrated in Figure 2, we found that there were 357 SNPs associated with Crohn's disease among the 10,000 SNPs with the highest eQTL function scores; the expected number, based on 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
