Table 1

Association analysis of T1D and CD associated SNPs in UK JIA case–control cohort

DiseaseSNPCHRPositionGeneMinoralleleMajoralleleMAFAFFMAFUNAFFCase 11 (%)Case 12 (%)Case 22 (%)Control 11 (%)Control 12 (%)Control 22 (%)ptrendOR (95% CI)
CDrs28163161192536813RGS1GT0.170.1827 (2.7)288 (29.2)672 (68.1)99 (3.4)835 (28.5)1993 (68.1)0.750.98 (0.85 to 1.12)
rs9179972103070568IL18RAPAG0.220.2260 (6.1)321 (32.5)606 (61.4)147 (5.0)1013 (34.6)1771 (60.4)0.971.00 (0.89 to 1.13)
rs6441961346352384CCR3TC0.320.3198 (9.9)431 (43.7)457 (46.3)280 (9.6)1239 (42.3)1409 (48.1)0.371.05 (0.94 to 1.17)
rs178105463159665050IL12AGA0.130.1219 (1.9)210 (21.3)756 (76.8)45 (1.5)616 (21.1)2264 (77.4)0.541.05 (0.90 to 1.23)
rs14645103188112554LPPTG0.480.44221 (22.4)512 (52.0)252 (25.6)617 (19.9)1524 (49.1)966 (31.1)0.0021.18 (1.06 to 1.30)
rs1824296159469574TAGAPAG0.450.45190 (19.3)500 (50.7)296 (30.0)590 (20.5)1421 (49.3)870 (30.2)0.690.98 (0.88 to 1.09)
rs65317812112007756SH2B3/ATXN2GA0.520.49265 (26.8)492 (49.8)230 (23.3)703 (24.1)1449 (49.6)771 (26.4)0.021.13 (1.02 to 1.25)
T1Drs19907602163124051IFIH1CT0.380.39145 (14.8)459 (46.7)379 (38.6)525 (15.3)1627 (47.3)1286 (37.4)0.500.97 (0.87 to 1.07)
rs11755527690958231BACH2GC0.490.46222 (22.5)520 (52.7)244 (24.7)669 (21.5)1551 (49.9)891 (28.6)0.061.10 (1.00 to 1.22)
rs689112182224INSTA0.290.2887 (8.8)402 (40.8)497 (50.4)254 (8.2)1246 (40.0)1612 (51.8)0.381.05 (0.94 to 1.18)
rs22922391256482180ERBB3AC0.350.35124 (12.6)430 (43.8)427 (43.5)432 (12.4)1558 (44.7)1498 (42.9)0.890.99 (0.89 to 1.10)
rs38259321579235446CTSHTC0.330.32117 (12.1)401 (41.3)452 (46.6)323 (10.4)1366 (44.1)1407 (45.4)0.851.01 (0.91 to 1.13)
rs37880132143841328UBASH3AAC0.420.43174 (17.7)486 (49.3)325 (33.0)590 (9.0)1522 (49.0)996 (32.0)0.380.95 (0.86 to 1.06)
  • AFF, affected; CD, coeliac disease; CHR, chromosome; JIA, juvenile idiopathic arthritis; MAF, minor allele frequency; SNP, single-nucleotide polymorphism; T1D, type 1 diabetes; UNAFF, unaffected.