The likelihood of a shared functional effect between a GWAS SNP (NHGRI database, accessed 21.12.10) and an eQTL was assessed by quantifying the change in the statistical significance of the eQTL after correcting for the effect of the GWAS SNP as previously described14. The ProbABEL associations of the eQTL genotype with the residuals from the standard linear regression of the “corrected-for” SNP against normalized expression values were re-done. The LD structure in each hotspot interval separately were accounted for by ranking (RankGWAS SNP) the impact on the eQTL (quantified by the adjusted association P-value after correction) of the GWAS SNP correction to that of correcting for all other SNPs in the same interval. By taking into account the total number of SNPs in the interval (NSNPs), this ranking across different genes and intervals can then be compared. For this purpose we define the regulatory trait concordance (RTC) Score ranked below ranging from 0 to 1, with values closer to 1 indicating causal regulatory effects.
