Further, we investigated the consistency of the eQTLs derived from the cohorts. Rather than simply comparing the existence of eQTLs, we adopted replication criteria similar to GWAS. A successful replication was defined as an eQTL in which the relationship between the same SNP and gene expression (with the same sign) was observed in more than one cohort at a P of ≤1×10−4. Using this criterion, 54.5% of the Laval cis-eQTLs were replicated in at least one other cohort and 79.5% of the Laval trans-eQTLs were replicated in another cohort. With respect to the Groningen eQTLs, the replication rates of the cis- and trans-eQTLs were 72.3% and 86.0%, respectively. The replication rates of the UBC cis- and trans-eQTLs were 65.4% and 90.5%, respectively. The eQTLs with higher R2values (variance of gene expression level explained) were more likely to be replicated than those with lower R2 values. There was a higher replication rate with trans-eQTLs than with cis-eQTLs.
