We further investigated the extent to which cis-eQTL signals operate in an exon-specific manner using a modified test of heterogeneity that accounts for the dependency structure arising from within-individual and within-gene correlations. We found that 86.45% of testable cis-eQTL subsignals were significantly heterogeneous across exons (Supplementary Table 5). We accept that this figure may be inflated by probe-specific artifacts. To moderate this, we only tested for heterogeneity among exons with evidence of expression, and we also performed rigorous quality control to remove array probes that might be influenced by sequence variation (see Online Methods for details). We anticipate that RNA-seq data will provide a more accurate figure for between-exons signal heterogeneity.
