Extended Data Figure 8. Tissue-specificity of cis- and trans-eQTLs.

a, Sharing of independently identified cis-eGenes across the 44 GTEx tissues (cis-eGenes are independently identified in each of the 44 tissues and then binned by the number of tissues in which they appear). b, Sharing of cis-eGenes across 44 GTEx tissues that were identified using the hierarchical multi-tissue analysis. c, The prior probabilities of having significant variant–gene association in different numbers of tissues, calculated using an empirical Bayes model. The prior probabilities are summed up on the basis of the Hamming weights of the corresponding cis-eQTL configurations. d–g, Meta-analysis performed using Meta-Tissue for trans-eGenes (50% FDR), randomly selected cis-eGenes (50 % FDR), and an equal number of the top cis-eGenes by P value. Distribution of the number of tissues that have Meta-Tissue m values greater than a given threshold (d, 0.5; e, 0.6; f, 0.9) across variant–gene pairs that have an effect (based on m value thresholding) in at least one tissue. g, The same distribution as d except that variant–gene pairs with predicted effect in zero tissues (based on the number of m values > 0.5) are included. Meta-Tissue predicts that many cis-eGenes (50% FDR) and trans-eGenes (50% FDR) will have an effect in zero tissues. The number of zero predictions is largely reduced for the top most significant cis-eGenes. h, Distribution of observed replication rate between pairs of tissues for trans-eQTLs (10% FDR) versus the predicted replication rate for trans-eQTLs (10% FDR) based on a negative binomial generalized linear model trained on cis-eQTLs (10% FDR0.1). This model directly accounts for effect size and minor allele frequency. Replication rates shown for a range of FDR thresholds in replication tissue. Box plots depict the IQR, whiskers depict 1.5× IQR.