To test the correlation between trans-eQTL effects in the discovery and replication datasets, we used the rb approach24, which accounts for the errors in the estimated eQTL effects so that the estimate of correlation is less dependent on sample sizes. First, we derived the estimate of the trans-eQTL effect (beta) and the standard error of the beta (SE(beta)) from the Z-score and the MAF of the significant trans-eQTLs, using the following formulae from Zhu et al. 201663 beta=z/(√(2p(1-p)(n+z2)) SE(beta)=1/(√(2p(1-p)(n+z2)) where p is the MAF, n is the sample size and z is the meta-analysis Z-score. MAF was computed from 26,609 eQTLGen samples (excluding FHS) for discovery analysis and from 1,139 replication samples for scRNA-seq replication analyses. For analyses in purified cell types and cell lines (LCL, iPSC) where allele frequencies were not available, we used the MAF as observed in eQTLGen instead.
