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. A total of 2,078 SNPs were identified with an MAF > 0.1, of which 1,011 were represented by a proxy on the Illumina genotyping chip (r 2 = 1 with the splicing SNP in Centre d'Etude du Polymorphisme Humain from Utah (CEU) HapMap samples). For both tissue types, fewer than 7% of consensus site SNPs associated with relevant exon expression levels (Table S4). While it is likely that some associations are missed because of unknown exons not included on the array, this number was surprisingly low given the common conception that disruption of this highly conserved region would very likely disrupt exon assembly. We emphasize that this analysis only evaluates systematically the effects of common SNPs in consensus regions at the exon boundaries and note that rare variation may produce profoundly different effects.
