In addition, there are a large number of genes showing differences in expression level between tissues11. It is not clear whether these differences are partly driven by the differences in eQTL effect. We sought to address this question by examining the correlation between test-statistic for difference in cis-eQTL effect (in SD units) and test-statistic for difference in mean expression level of the corresponding gene (in log2(RPKM) units) between GTEx-cerebellum and GTEx-blood for the 3569 genes each with a cis-eQTL at PeQTL < 5 × 10−8 in GTEx-muscle (Supplementary Table 2). Note that the cis-eQTL effects were re-scaled based on the expression level per gene in SD units so that the correlation was not confounded by the mean–variance relationship in gene expression. That is, if the difference in eQTL effect and that in expression level were both computed in RPKM units, genes with larger differences in mean between tissues are more likely to have differences in variance because of the mean–variance relationship, giving rise to differences in eQTL effect even if the eQTL effects are not different in SD units. We
