Comparison of Genome-wide Association Study-identified Loci with ENCODE DataPanel A shows overlap of lead SNPs in the NHGRI GWAS SNP catalog (June 2011) with DHSs (left) or TF-binding sites (right) as red bars compared to various control SNP sets in blue. The control SNP sets are: SNPs on the Illumina 2.5M chip as an example of a widely used GWAS SNP typing panel; SNPs from the 1,000 Genomes project; SNPs extracted from 24 personal genomes (see Personal Genome Variants track at http://main.genome-browser.bx.psu.edu80 all shown as blue bars. In addition a further control utilised 1,000 randomisations from the genotyping SNP panel, matching the SNPs with each NHGRI catalog SNP for allele frequency and distance to the nearest TSS (light blue bars with bounds at 1.5 times the interquartile range, and any outliers beyond shown as circles). For both DHSs and TF binding regions, a larger proportion of overlaps with GWAS-implicated SNPs is found compared to any of the controls sets. Panel B shows the aggregate overlap of phenotypes to selected TF-binding sites (left matrix) or DHSs in selected cell lines (right matrix), with a count of overlaps between the phenotype and the cell line/factor. Values in green squares pass an empirical p-value threshold <=0.01 (based on the same analysis of overlaps between randomly chosen, GWAS-matched SNPs and these epigenetic features) and have at least a count of 3 overlaps. The p-value for the total number of phenotype-TF associations is <0.001. Panel C shows several SNPs associated with Crohn’s disease and other inflammatory diseases that reside in a large gene desert on chromosome 5, along with some epigenetic features suggestive of function. The SNP (rs11742570) strongly associated to Crohn’s disease overlaps a GATA2 TF binding signal determined in HUVEC cells. This region is also DNaseI hypersensitive in HUVEC and T-helper Th1 and Th2 cells.
