SNPs that are located within two base pairs of an intron–exon junction, or located at exonic splicing enhancer (ESE) or exonic splicing silencer (ESS)-binding sites may disrupt mRNA splicing and severely affect protein function (15). We predicted ESE and ESS sites using procedure outlined in Supplementary Figure 2. If an exon was longer than 140 base pairs, only SNPs within the first and last 70 base pairs of each exon were evaluated because the effect of alternative alleles on the activity of ESEs and ESSs decrease with distance from the splice site (16,17). We only considered a maximum of 10 base pairs on either side of a SNP because there are no significant compensatory or correlated relationships between non-overlapping ESE or ESS motifs (18). ESE sites were predicted using RESCUE ESE (19) or ESEfinder (20) methods. ESS sites were predicted using the FAS–ESS (21) method. A SNP was classified as affecting splicing activity if there was at least one predicted binding site with one allele, but none with the other allele. In order to reduce false positive results, we excluded
