This scan of genome-wide associations for effects on expression changes also identified splicing effects of rs6678677, a SNP originally identified as a risk factor in rheumatoid arthritis and later a contributor to type 1 diabetes predisposition, in the PTPN22 gene [12,19–21]. We note that the associated SNP is located directly in the region targeted by the associated probeset, which may result in a false positive association, however the SNP effects were not observed in the brain tissue despite a similar expression level in the minor allele homozygotes. Additional work is needed to confirm this association.
