in the second step together with posterior genotypic probabilities performing the score test in ProbABEL 36, using the “—mmscore” option. In total, 776 adipose, 777 LCL and 667 skin samples had both expression profiles and imputed genotypes and were included in the analysis. Cis analysis was limited to SNPs located within 1MB either side of the transcription start or end site or within the gene body. False discovery rate (FDR) for the cis analysis was calculated from the complete list of p values using the qvalue package20 implemented in R2.11 37. In order to characterize likely independent regulatory effects, the identified cis-eQTLs were mapped to recombination hotspot intervals 38. For each gene, the most significant SNP per hotspot interval were selected followed by additional LD filtering (for each remaining SNP pair with D’ > 0.5 and r2>0.1 the least significant SNP was ignored).
