Interpreting T1DM GWAS findings at 4q27 using fitSNPs. The region 4q27 has been identified as a risk factor area for T1DM, celiac disease, and rheumatoid arthritis. IL2, IL21, and TENR were selected based on prior knowledge for sequencing in the follow-up studies, but no association was found. KIAA1109 has a much higher fitSNPs DER value than all other genes in the region, and is flanked by two significant T1DM GWAS SNPs (-log10P >5). We predicted that this gene may explain the T1DM association in this region. The GWAS -log10P curve for KIAA1109 is missing because it was not listed in the Affymetrix 500 K SNP array used for the GWAS. DER, differential expression ratio; fitSNPs, functionally interpolating single nucleotide polymorphisms; GWAS, genome-wide association study; SNP, single nucleotide polymorphism; T1DM, type 1 diabetes mellitus.
Chen et al. Genome Biology 2008 9:R170 doi:10.1186/gb-2008-9-12-r170