Analyses on other phenotypes from the WTCCC association studies [11] confirmed that our proposed annotations benefit phenotypes beyond Crohn's disease. Figure 4 illustrates that both type 1 diabetes (T1D) and rheumatoid arthritis (RA) had significantly more SNPs than expected with phenotype associations (p<.01) among the 10,000 SNPs with top eQTL function scores. To insure that these results were not driven by strong LD among SNPs in the major histocompatibility complex (MHC) region, we repeated the analyses for all Wellcome Trust phenotypes after removing all SNPs on chromosome 6, with substantially similar results. Figure 5 highlights the enrichment of functional SNPs (eQTL function scores larger than 3) among the SNPs with the strongest associations to disease in the scans for T1D and RA (not unexpected given results in Figure 4), but also for hypertension and bipolar disease. There is little evidence for enrichment of eQTLs among top signals for coronary artery disease (CAD) or type 2 diabetes (T2D). These results suggest that for at least some complex traits, a more efficient prioritization for replication studies can be achieved by incorporating the
