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 predicted binding sites within an exon if, based on Ensembl transcripts isoform data, there were no alternatively spliced transcripts observed involving the exon. For example, suppose a gene has eight exons and five different transcript isoforms reported in Ensembl. If there was a predicted ESE or ESS-binding site in exon 3 but all five transcripts include exon 3, then we would exclude the site.
