We speculated that the locations of exon-specific and gene-level cis-eQTL signals may differ as a result of the different regulatory mechanisms that may be involved. We found that gene-level cis-eQTL signals were symmetrically distributed around the transcription start site, while exon-specific signals tended to be located within the gene itself, as indicated by a positive shift in the marker distribution (Fig. 5c; two-sample Kolmogorov-Smirnov P = 1.6 × 10−10). However, we did not find any significant differences in the genic location of variants involved in gene-level cis-eQTL signals as compared to exon-specific cis-eQTL signals (Fig. 5d).
