We tested the replication of the 59,786 discovery trans-eQTLs only if the trans-eQTL gene was sufficiently expressed (i.e. had a missing sample fraction that was at most 20% in the large OneK1K dataset), leaving between 1,917 and 27,582 eQTLs to be studied, depending on cell type. We estimated the inflation of signal by calculating the lambda inflation relative to the inverse chi-square cumulative distribution function of 0.5. Trans-eQTLs with FDR<0.05 in any cell type were deemed significantly replicating. To get a better idea of replication across cell types, we calculated the average Z-score across cell types. We selected effects with an absolute average Z-score>1.96 (equivalent to P<0.05) to calculate the allelic concordance with the discovery trans-eQTLs.
