Bioinformatic pipeline used to predict splice site SNPs that are associated with autoimmune diseases and inflammatory traits. Index inflammatory SNPs were identified that had been associated by GWAS with susceptibility to autoimmune diseases and inflammatory traits. The proxies to these GWAS SNPs were pulled using the SNAP Proxy Search tool (Broad Institute). The ‘functional consequence to transcript’ for each SNP was identified as being ‘Splice Site’ or ‘Essential Splice Site’ using the Biomart function of Ensembl. These SNPs were then bioinformatically analysed to predict whether a splicing change was likely to occur, using the programmes ESE finder (web-based tool that predicts ESE element sequences that are bound by SR proteins), NNSplice (web-based tool that algorithmically predicts core spice site sequences in a given sequence) and Alamut (splicing mutation prediction programme that amalgamates predictions from five different splice site prediction algorithms to identify potential core splice sites in a given gene transcript). A subset of SNPs was then prioritised for further analysis of their splicing by RT-PCR. The numbers in brackets denote how many SNPs were identified at each stage.