Association analysis in JIA cases and controls of SNPs previously associated with RA
| Marker | Chromosome | Locus | HWE controls | MAF cases | MAF controls | Genotype frequency cases (%) | Genotype frequency controls (%) | Trend p value | Allelic OR (95% CI) | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| rs10910099 | 1 | MMEL | 0.27 | 0.34 | 0.33 | 90 (10.3) | 412 (47.2) | 371 (42.5) | 401 (11.0) | 1572 (43.1) | 1672 (45.9) | 0.28 | 1.06 (0.95 to 1.19) |
| rs11889341 | 2 | STAT4 | 0.69 | 0.26 | 0.22 | 54 (5.7) | 376 (54.4) | 512 (54.4) | 162 (4.6) | 1200 (34.4) | 2125 (60.9) | 0.0004 | 1.24 (1.1 to 1.39) |
| rs7574865 | 2 | STAT4 | 0.62 | 0.26 | 0.22 | 52 (5.5) | 378 (40.1) | 513 (54.4) | 161 (4.6) | 1208 (34.3) | 2151 (61.1) | 0.0004 | 1.24 (1.1 to 1.39) |
| rs8179673 | 2 | STAT4 | 0.62 | 0.26 | 0.22 | 55 (5.9) | 378 (40.2) | 507 (53.9) | 162 (4.7) | 1198 (34.6) | 2103 (60.7) | 0.0002 | 1.25 (1.11 to 1.4) |
| rs10181656 | 2 | STAT4 | 0.52 | 0.26 | 0.22 | 54 (5.7) | 377 (40.1) | 509 (54.1) | 159 (4.6) | 1200 (34.5) | 2115 (60.9) | 0.0002 | 1.24 (1.11 to 1.4) |
| rs6920220 | 6 | 6q23/TNFAIP3 | 0.04 | 0.24 | 0.21 | 57 (6.5) | 297 (34.0) | 519 (59.5) | 140 (3.8) | 1251 (34.3) | 2253 (61.8) | 0.02 | 1.16 (1.02 to 1.31) |
| rs13207033 | 6 | 6q23/TNFAIP3 | 0.5 | 0.25 | 0.28 | 64 (7.1) | 327 (36.3) | 511 (56.7) | 229 (7.6) | 1237 (40.8) | 1563 (51.6) | 0.02 | 0.87 (0.77 to 0.98) |
| rs42041 | 7 | CDK6 | 0.66 | 0.26 | 0.25 | 65 (7.0) | 347 (37.5) | 514 (55.5) | 182 (6.1) | 1125 (38.0) | 1655 (55.9) | 0.59 | 1.03 (0.92 to 1.16) |
| rs3761847 | 9 | TRAF1/C5 | 0.39 | 0.44 | 0.43 | 199 (21.1) | 438 (46.5) | 305 (32.4) | 607 (18.8) | 1557 (48.2) | 1063 (33.0) | 0.27 | 1.06 (0.96 to 1.18) |
| rs10818488 | 9 | TRAF1/C5 | 0.81 | 0.45 | 0.43 | 201 (21.3) | 451 (47.8) | 291 (30.9) | 645 (18.5) | 1721 (49.3) | 1126 (32.2) | 0.1 | 1.09 (0.98 to 1.21) |
| rs2900180 | 9 | TRAF1/C5 | 0.97 | 0.39 | 0.35 | 149 (15.8) | 437 (46.4) | 356 (37.8) | 407 (11.9) | 1548 (45.3) | 1464 (42.8) | 0.0003 | 1.21 (1.09 to 1.35) |
| rs2812378 | 9 | CCL21 | 0.30 | 0.33 | 0.35 | 88 (9.5) | 433 (46.5) | 410 (44.0) | 377 (12.5) | 1339 (44.5) | 1294 (43.0) | 0.1 | 0.91 (0.82 to 1.02) |
| rs4750316 | 10 | PRKCQ | 0.91 | 0.18 | 0.2 | 38 (4.0) | 256 (27.2) | 649 (68.8) | 133 (3.8) | 1106 (31.6) | 2261 (64.6) | 0.05 | 0.88 (0.77 to 1.0) |
| rs1678542 | 12 | KIF5A | 0.39 | 0.35 | 0.37 | 109 (11.6) | 438 (46.5) | 394 (41.9) | 497 (14.1) | 1622 (45.9) | 1411 (40.0) | 0.08 | 0.91 (0.82 to 1.01) |
| rs4810485 | 20 | CD40 | 0.05 | 0.26 | 0.25 | 64 (6.9) | 351 (37.9) | 512 (55.2) | 173 (5.7) | 1189 (39.1) | 1681 (55.2) | 0.59 | 1.03 (0.92 to 1.16) |
SNPs with a trend p value <0.05 are highlighted in bold.
HWE, Hardy–Weinberg equilibrium; JIA, juvenile idiopathic arthritis; MAF, minor allele frequency; OR, odds ratio; SNP, single nucleotide polymorphism.