One possible explanation for tissue-specific eQTLs is tissue-specific expression; that is, if a gene is strongly expressed only in one tissue, this could cause an eQTL for that gene to show a strong effect only in that tissue. Whether or not a tissue-specific eQTL is due to tissue-specific expression could considerably impact biological interpretation. To assess whether tissue-specific eQTLs could be explained by tissue-specific expression we took genes with tissue-specific eQTLs and examined the distribution of expression in the eQTL-affected tissue relative to expression in other tissues. We found this distribution to be similar to genes without tissue-specific eQTLs (Supplementary Fig. 8). Therefore, most tissue-specific eQTLs identified here do not solely reflect tissue-specific expression.
