Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data.

(Note that the RNA-seq analysis of splicing-QTLs is thought to be underpowered in this data set, except for the most highly expressed genes (see Supplementary Figure 15 of [13] ), which may explain why the enrichment of last-exon QTLs is lower for the RNA-seq data than for the Affymetrix data.) As an illustration, Figure 4 provides an example of a highly significant Illumina eQTL (p = ), for which the most significant SNP lies within the 3′ UTR.

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