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 found that the correlation was marginal (r = 0.003) (Fig. 3). This is analogous to the observation that there is a large difference in mean height between men and women but the effects of all autosomal SNPs on height in men are almost identical to those in women32,33. However, these results also suggest that an eQTL with identical effect on gene expression in SD units in different tissues could show different effects in RPKM units if the variance of gene expression varies across tissues, which might explain the results from recent studies that genetic variants in or near genes differentially expressed in a particular tissue are enriched for associations with a complex trait34,35.
