As an alternative strategy for comparing eQTLs among different tissues, we also calculated the π1 statistic (π1 = 1 - π0; 75) for all pairs of tissues (Extended Data Fig. 8b) using the qvalue package in R. The π1 statistic provides a global measure of similarity between a pair of tissues by estimating the proportion of eQTL signal discovered in one tissue that shows evidence of replication in a second tissue. For this analysis, for each discovery tissue, we queried all significant variants per eGene in the full cis output of all other tissues and estimated q0 with the ‘bootstrap’ method of the qvalue package.
