We examined the enrichment of internal cis-eQTL signals within genic regions (promoter, coding, intronic or untranslated regions (UTRs)) relative to external cis-eQTL signals that were also annotated to a gene (though by definition not the gene they regulate). We found a relative increase in the frequency of internal cis-eQTL signals mapping to promoter or coding regions but, most prominently, UTRs (P = 0.0026; Fig. 6b). This pattern suggests that internal cis-eQTL signals may act more by changing the rate of mRNA degradation than by changing the rate of transcription per se. To investigate this further, we looked at whether the gene targets of internal cis-eQTL signals were enriched for specific sequence features that are already known to influence mRNA decay, such as AU-rich elements and microRNA binding site densities. We found a significant enrichment of genes containing AU-rich elements (as defined by the AREsite database31, http://rna.tbi.univie.ac.at/cgi-bin/AREsite.cgi) among the gene targets of internal cis-eQTL signals (Fisher’s exact P = 7.46 × 10−10) but no significant difference in miRNA binding site densities (two-sample Kolmogorov-Smirnov P = 0.072). Therefore, while complexity in the
