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. Both the fixed effect and random effect meta-analysis results are presented in Table S2, and we used the fix effect results in the downstream analysis. We previously showed that the number of eQTLs detectable at a certain FDR was related directly to the sample size (i.e. statistical power) [21]. The meta-analysis yielded a greater relative increase in the number of trans activating eQTLs than of cis-eQTLs, suggesting that sample size is particularly important for detecting trans-eQTLs. Among the 51,627 non-control probesets on our array, 33.0% showed a cis-eQTL. 74.0%, 64.4%, 56.4% of the 51,627 probesets were “present” in at least 20%, 50%, and 80% of the tissue samples. Using these three cutoffs, 40.2%, 42.5%, and 43.4% of the “present” transcripts were found to be controlled by cis-eSNPs, respectively. Accordingly we believe that we have identified the majority of the strong lung cis-eQTLs.
