Amongst all the study-wide significant sQTLs, only two of them are themselves located in a consensus splicing sequence for the relevant exons, rs10814567 in POLRE1 and rs7770794 in PIP3-E. We note, however, that the probeset screening for the associated exon in POLRE1 contains a SNP in perfect LD with the consensus site SNP and therefore may be the result of poor hybridization to the target. Given that most common polymorphisms are now known, it is surprising that there are so few cases where a candidate polymorphism responsible for a splicing change is in the consensus sequence, although this scarcity may be due to low primary representation of these SNPs on the array. To further evaluate the role of polymorphisms in consensus sequences, we identified all known polymorphisms in the conserved region located at the exon boundaries of the close to 300,000 core exons measured on the Affymetrix array (three basepairs into the exon and eight into the intron, Ensembl database, National Center for Biotechnology Information [NCBI] Build 36 hg18) and assessed how these influenced the expression levels of neighboring exons.
