To screen for effects of consensus site SNPs, we first identified all known SNPs located in highly conserved consensus site regions at the exon-intron boundary including all SNPs eight basepairs into an intron and three basepairs into an exon (Ensembl database). A total of 2,078 common consensus site SNPs were identified, of which 1,011 had proxies (r 2 = 1) with one or more SNPs on the Illumina Human Hap550K chip allowing assessments of their effects in the present dataset. Specifically, consensus site SNPs, or their proxies, were assessed for significant associations (uncorrected p < 0.05) with the expression level of the immediate exon or exons located up- or downstream for all transcripts containing that exon.
