Summary of transcribed and DHSP overlapping genetic variation identified in ST8SIA2.

The location of transcribed and DHSP overlapping variants on chromosome 15 (hg19 build), with transcribed SNPs indicated with asterisks. SNP alleles (mA) identified exclusively on the risk haplotype are shown (0 = not exclusive, 1 = present on risk and other haplotypes, 2 = present on risk haplotype only, ND = not determined). SNPs identified exclusively on the protective haplotype are shown (0 = not exclusive, 1 = present on protective and other haplotypes, 2 = present on protective haplotype only, ND = not determined). The set from which the SNP was observed is given (1 = GATK & Refmapper; 2 = GATK only; 3a = Refmapper only; 3b = Refmapper only & filtered in GATK; 4 = Sanger). Co-localisation with DNase I hypersensitivity site (DHS) peaks (neuronal = 1; hESC = 2; foetal brain = 3) are given. Genomic Evolutionary Rate Profiling (GERP) scores are provided for each variant that is within a GERP-conserved element. The nature of the polymorphism in each cohort is given (with minor allele listed first). The minor allele frequency (MAF) of each variant in the 47 bipolar cases and 174 Caucasian individuals (CEU and GBR) from the 1000 Genomes Project (1 kG) are shown separately. The frequency difference (freqDIFF) was calculated relative to 1 kG allele frequency, with absolute frequency differences greater than 5% indicated in bold text, and those with p values aFor each polymorphism, the minor allele is listed first.vSNPs verified by direct genotyping are indicated. The annotated list of all ST8SIA2 variation identified is given in Table S1.