Seven T1D-associated SNPs (GLIS3/rs7020673, BACH2/rs11755527, SKAP2/rs7804356, GDSMB/rs2290400, C6orf173/rs9388489, LOC399716/rs947474 and DLK1-MEG2/rs941576) were genotyped in a large Pakistani RA case–control sample (n = 1959) using TaqMan® SNP genotyping assays. Here, PTPN9 is linked to rheumatoid arthritis.