We identified cis- and trans-acting eQTLs using established methods [19]. For simplicity we assumed that each transcript could have at most one cis-eQTL. We considered all association signals from SNPs within 1 Mb up and downstream, of the transcription probeset as a single cis-eQTL. Trans-eQTLs were defined as association signals from SNPs located greater than 1 Mb from the probeset. The eSNP was identified as the SNP that was most significantly associated (lowest P value) with the expression trait. A summary of the eQTLs identified at 10% false discovery rate (FDR) in the three cohorts as well as the meta-analysis are reported in Table 2. There were variations in the numbers of eQTLs across the cohorts. For example, we identified 10,630, 5,655 and 7,953 cis-eQTLs in the Laval, Groningen and UBC cohorts, respectively. There were also variations in the number of detectable trans-eQTLs (Table 2). The P values reported for the trans-eQTLs are lower than those for cis-eQTLs, owing to the higher statistical threshold required to achieve statistical significance. In general, a single SNP (eQTL peak) explained between 10 and
