RA-associated SNP nominally associated with JIA (all JIA subtypes) (p≤0.05)
| SNP | CHR | Position | Gene | Minor allele | Major allele | MAF cases | MAF controls | HWE controls | Case 11 (%) | Case 12 (%) | Case 22 (%) | Control 11 (%) | Control 12(%) | Control 22 (%) | pTREND | OR 95% CI |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| rs4272626 | 1 | 116149950 | NHLH2 | T | C | 0.34 | 0.36 | 0.79 | 517 (44.2) | 511 (43.7) | 142 (12.1) | 3264 (40.8) | 3702 (46.3) | 1035 (12.9) | 0.05 | 0.91 (0.83 to 1.00) |
| rs11586238 | 1 | 117064661 | CD2 | G | C | 0.26 | 0.24 | 0.48 | 636 (54.4) | 455 (38.9) | 79 (6.8) | 4586 (57.3) | 2957 (37.0) | 456 (5.7) | 0.03 | 1.11 (1.01 to 1.23) |
| rs1773560 | 1 | 165688387 | CD247 | G | A | 0.38 | 0.42 | 0.48 | 456 (39.2) | 520 (44.7) | 187 (16.1) | 2652 (33.4) | 3849 (48.5) | 1443 (18.2) | 0.0003 | 0.85 (0.78 to 0.93) |
| rs10919563 | 1 | 196967065 | PTPRC | A | G | 0.09 | 0.13 | 0.92 | 917 (83.0) | 171 (15.5) | 17 (1.5) | 5994 (75.3) | 1824 (22.9) | 137 (1.7) | 2.57×10−7 | 0.67 (0.58 to 0.78) |
| rs874040 | 4 | 25717295 | RBPJ | G | C | 0.33 | 0.30 | 0.62 | 445 (44.4) | 451 (45.0) | 107 (10.7) | 3938 (48.7) | 3401 (42.0) | 754 (9.3) | 0.01 | 1.14 (1.03 to 1.26) |
| rs13119723 | 4 | 123437763 | IL2_IL21 | G | A | 0.13 | 0.16 | 0.24 | 721 (76.0) | 204 (21.5) | 24 (2.5) | 5631 (71.0) | 2090 (26.3) | 214 (2.7) | 0.004 | 0.81 (0.71 to 0.93) |
| rs10040327* | 5 | 55470977 | ANKRD55 | A | C | 0.09 | 0.11 | 0.20 | 825 (82.4) | 167 (16.7) | 9 (0.9) | 6417 (79.1) | 1583 (19.5) | 112 (1.4) | 0.01 | 0.81 (0.69 to 0.95) |
| rs26232 | 5 | 102624619 | C5orf30 | T | C | 0.29 | 0.33 | 0.35 | 506 (50.4) | 417 (41.6) | 80 (8.0) | 3579 (45.0) | 3536 (44.5) | 831 (10.5) | 0.0003 | 0.83 (0.75 to 0.92) |
| rs10488631 | 7 | 128381419 | IRF5 | C | T | 0.13 | 0.11 | 0.47 | 902 (76.5) | 257 (21.8) | 20 (1.7) | 4119 (79.6) | 1003 (19.4) | 54 (1.0) | 0.009 | 1.20 (1.05 to 1.37) |
| rs2736340 | 8 | 11381382 | BLK | T | C | 0.27 | 0.24 | 0.88 | 522 (52.4) | 406 (40.8) | 68 (6.8) | 4631 (57.1) | 3002 (37.0) | 481 (5.9) | 0.006 | 1.16 (1.04 to 1.28) |
| rs706778 | 10 | 6138955 | IL2RA | T | C | 0.45 | 0.40 | 0.80 | 314 (31.4) | 479 (47.9) | 208 (20.8) | 2926 (36.1) | 3883 (47.9) | 1304 (16.1) | 5.61×10−5 | 1.21 (1.10 to 1.33) |
| rs2872507 | 17 | 35294289 | ORMDL3 | A | G | 0.52 | 0.48 | 0.75 | 221 (23.2) | 474 (49.8) | 256 (26.9) | 2199 (27.3) | 4001 (49.7) | 1846 (22.9) | 0.0009 | 1.18 (1.07 to 1.29) |
| rs7234029 | 18 | 12867060 | PTPN2 | G | A | 0.19 | 0.16 | 0.33 | 766 (65.5) | 362 (30.9) | 42 (3.6) | 5682 (71.1) | 2127 (26.6) | 182 (2.3) | 1.25×10−5 | 1.28 (1.15 to 1.43) |
↵* r2=0.86 with rs6859219 the single-nucleotide polymorphism (SNP) genotyped in the study by Stahl et al.12
Case 11, case genotype counts and percentage of major allele homozygotes; Case 12, case genotype counts and percentage of heterozygotes; Case 22, case genotype counts and percentage of minor allele homozygotes; Control 11, control genotype counts and percentage of major allele homozygotes; Control 12, control genotype counts and percentage of heterozygotes; Control 22, control genotype counts and percentage of minor allele homozygotes, p value for deviation from HWE. CHR, chromosome; HWE, Hardy–Weinberg equilibrium; JIA, juvenile idiopathic arthritis; MAF, minor allele frequency; pTREND, p value for the Armitage test for trend as generated in PLINK; RA, rheumatoid arthritis.