To test the utility of the SNPExpress database, we evaluated the 84 variants (Table S5) for localized associations within the transcript/exon containing this SNP or transcripts/exons within 100 kb of the SNP and determined thirteen to have a strong (p < 1 × 10−5) effect on an exon or transcript-level expression level (Figure 5, top panel; Table 3). Of these, rs11171739, associated with type 1 diabetes [12], was found through the use of an Illumina proxy to have an association with the exon-level expression of the RPS26 gene. In a follow-up analysis, a SNP in LD with rs11171739 (rs2292239 r 2 = 0.71 with rs11171739) was found to be more highly associated with type 1 diabetes [19]. Interestingly, a SNP located upstream of both of these SNPs, rs10876864, was found in our dataset to have the strongest association with a splicing event in RPS26. This observation extends what was recently reported by Schadt et al. [9] by specifically identifying RPS26 splicing as responsible for the expression association with the implicated polymorphism in type 1 diabetes. More generally, however, these results
