Figure 5. SNPs with the strongest evidence for association with WTCCC T1D, RA, hypertension, and bipolar disorder are more likely to have eQTL function scores >3.

The plots show results of eQTL enrichment analysis for the remaining Wellcome Trust phenotypes beginning with the SNPs most strongly associated with disease (similar to analyses for Crohn's disease summarized in Figure 3). For each disease, SNPs have been ordered according to their association p-values from the most to the least significant, and divided in groups of 10,000. For each group, the number of SNPs with expression score larger than 3 was calculated and the results are shown in the scatterplots. The horizontal lines illustrate the expectation based on the observed scores in all SNPs in the relevant WTCCC dataset. The dotted lines represent estimated 95% confidence bands obtained using simulations.