We observed a similar enrichment if we start with the SNPs most strongly associated with Crohn's disease and ask whether there was enrichment for SNPs with high eQTL function scores. As illustrated in Figure 3, in the top 1000 Crohn's associated SNPs we observed 392 with eQTL functional scores larger than 1 (the expected number based on all HapMap scores is 183.5), 324 SNPs with scores larger than 2 (143.5 expected by chance) and 172 with scores larger than 3 (with only 18.6 expected by chance). Among these 172 SNPs we observed some, such as in STAT3, that have been confirmed in replication studies.
