The meta-analysis revealed many more eQTLs owing to the increased sample size (Table 2). We identified 17,049 cis-eQTLs and 534 trans-eQTL and the details of all eQTLs are listed in Table S2. 68.7% of these cis-eQTLs and 31.7% of trans-eQTLs were identified in at least one cohort, suggesting that the meta-analysis detected many additional eQTLs. The ‘non-combinability’ among cohorts is quantified in terms of Cochran's Q and the τ statistics (Table S2). Cochran's Q, was calculated as the weighted sum of squared differences among individual study effects and the pooled effect across studies, with the weights proportional to the inverse of variance of the eQTL effect. Q follows a chi-square statistic with k-1 degrees of freedom (k is the number of studies), and by these means, we calibrated the p value (termed Q.pvalue). We detected modest degrees of heterogeneity among the three cohorts. 16% of the QTLs had Q.pvalue<0.05 and 2% of the eQTLs showed Q.pvalue<0.001. We also present the τ statistic, which is the moment-based estimate of the between-study variance and is not dependent on the number of studies.
