A replication profile was derived for each eGene in the discovery tissue, indicating whether the lead eQTL effect replicated (yes | no) or could not be tested (‘NA’). We then extracted eGenes, for which the lead eQTL effect did not show evidence of replication in any other tissue (P > 2.2x10-04) or could not be tested (hereon referred to as ’tissue-specific eQTLs’). Of note, in this analysis, for an eQTL effect to replicate, it has to affect the expression of the same gene in both tissues. It the same variant is an eQTL for two different genes in the two tissues, it is not considered replicating. We also investigated the impact of the specific replication threshold, considering a threshold of P<0.01 and P<0.05 (Extended Data Fig. 8c). This analysis showed that the ability to replicate an eQTL signal in a second tissue is primarily determined by the sample size of the replication tissue and not the specific choice of threshold. This dependency needs to be taken into account when interpreting tissue-specific eQTL effects.
