Table 3.
DAS28 response data by genotype and association p values for 17 successfully genotyped SNPs in 1012 individuals
| First cohort (n=1012) | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Additive model | Dominant model* | ||||||||||||||||||
| SNP | Gene | Chr | bp | Genotype | Count | Mean baseline DAS28 | SD baseline DAS28 | Mean change in DAS28 | SD change in DAS28 | HWE exact p value | Genotypic global p value | Global p value | Coef | Min 95 | Max 95 | Global p value | Coef | Min 95 | Max 95 |
| rs10865035 | AFF3 | 2 | 100202166 | AA | 240 | 6.72 | 1.02 | −2.28 | 1.57 | 0.089 | 0.051 | 0.018 | −0.16 | −0.29 | −0.03 | 0.024 | −0.25 | −0.46 | −0.03 |
| AG | 532 | 6.69 | 0.96 | −2.51 | 1.51 | ||||||||||||||
| GG | 237 | 6.68 | 0.99 | −2.58 | 1.63 | ||||||||||||||
| rs1160542 | AFF3 | 2 | 100198587 | AA | 247 | 6.70 | 0.97 | −2.59 | 1.61 | 0.050 | 0.066 | 0.022 | 0.15 | 0.02 | 0.29 | 0.101 | 0.17 | −0.03 | 0.38 |
| AG | 530 | 6.69 | 0.96 | −2.49 | 1.51 | ||||||||||||||
| GG | 221 | 6.68 | 1.00 | −2.25 | 1.56 | ||||||||||||||
| rs7574865 | STAT4 | 2 | 191672878 | GG | 564 | 6.73 | 0.99 | −2.57 | 1.55 | 0.400 | 0.051 | 0.094 | 0.13 | −0.02 | 0.28 | 0.028 | 0.20 | 0.02 | 0.39 |
| GT | 389 | 6.65 | 0.95 | −2.33 | 1.58 | ||||||||||||||
| TT | 57 | 6.64 | 1.10 | −2.49 | 1.40 | ||||||||||||||
| rs10181656 | STAT4 | 2 | 191678124 | CC | 563 | 6.73 | 0.99 | −2.57 | 1.54 | 0.559 | 0.067 | 0.122 | 0.12 | −0.03 | 0.27 | 0.038 | 0.19 | 0.01 | 0.37 |
| CG | 389 | 6.65 | 0.95 | −2.33 | 1.60 | ||||||||||||||
| GG | 60 | 6.63 | 1.07 | −2.50 | 1.37 | ||||||||||||||
| rs231775 | CTLA4 | 2 | 204440959 | AA | 365 | 6.68 | 1.00 | −2.50 | 1.53 | 0.794 | 0.775 | 0.500 | 0.04 | −0.09 | 0.17 | 0.484 | 0.07 | −0.12 | 0.25 |
| AG | 482 | 6.69 | 0.98 | −2.44 | 1.52 | ||||||||||||||
| GG | 165 | 6.73 | 0.94 | −2.52 | 1.72 | ||||||||||||||
| rs3087243 | CTLA4 | 2 | 204447164 | GG | 340 | 6.67 | 0.97 | −2.53 | 1.64 | 0.948 | 0.712 | 0.570 | 0.04 | −0.09 | 0.17 | 0.427 | 0.08 | −0.11 | 0.27 |
| GA | 492 | 6.74 | 0.96 | −2.46 | 1.49 | ||||||||||||||
| AA | 176 | 6.61 | 1.05 | −2.41 | 1.57 | ||||||||||||||
| rs6822844 | IL2–IL21 | 4 | 123728871 | GG | 725 | 6.69 | 0.95 | −2.45 | 1.58 | 0.151 | 0.376 | 0.317 | −0.09 | −0.26 | 0.08 | 0.208 | −0.13 | −0.33 | 0.07 |
| GT | 254 | 6.68 | 1.05 | −2.52 | 1.50 | ||||||||||||||
| TT | 31 | 7.00 | 0.84 | −2.70 | 1.33 | ||||||||||||||
| rs13192841 | TNFAIP3 | 6 | 138008907 | GG | 577 | 6.66 | 0.98 | −2.50 | 1.59 | 0.672 | 0.406 | 0.469 | 0.05 | −0.09 | 0.20 | 0.271 | 0.10 | −0.08 | 0.28 |
| GA | 371 | 6.72 | 0.99 | −2.41 | 1.51 | ||||||||||||||
| AA | 64 | 6.77 | 0.92 | −2.60 | 1.48 | ||||||||||||||
| rs6920220 | TNFAIP3 | 6 | 138048197 | GG | 525 | 6.69 | 0.96 | −2.49 | 1.49 | 0.430 | 0.536 | 0.314 | 0.07 | −0.07 | 0.22 | 0.265 | 0.10 | −0.08 | 0.28 |
| GA | 413 | 6.69 | 1.00 | −2.44 | 1.61 | ||||||||||||||
| AA | 71 | 6.68 | 1.02 | −2.43 | 1.68 | ||||||||||||||
| rs5029937 | TNFAIP3 | 6 | 138236844 | GG | 900 | 6.67 | 0.98 | −2.44 | 1.54 | 0.763 | 0.463 | 0.216 | −0.18 | −0.47 | 0.11 | 0.227 | −0.18 | −0.48 | 0.11 |
| GT | 105 | 6.91 | 0.92 | −2.73 | 1.64 | ||||||||||||||
| TT | 2 | 7.46 | 0.35 | −3.43 | 1.01 | ||||||||||||||
| rs2812378 | CCL21 | 9 | 34700260 | TT | 379 | 6.67 | 1.02 | −2.42 | 1.53 | 0.386 | 0.876 | 0.637 | −0.03 | −0.17 | 0.10 | 0.609 | −0.05 | −0.24 | 0.14 |
| TC | 490 | 6.70 | 0.95 | −2.51 | 1.56 | ||||||||||||||
| CC | 140 | 6.74 | 0.96 | −2.48 | 1.62 | ||||||||||||||
| rs10760130 | TRAF1 | 9 | 122741811 | AA | 313 | 6.71 | 0.99 | −2.39 | 1.58 | 0.798 | 0.457 | 0.981 | 0.00 | −0.13 | 0.13 | 0.520 | −0.06 | −0.26 | 0.13 |
| AG | 492 | 6.68 | 0.94 | −2.54 | 1.53 | ||||||||||||||
| GG | 200 | 6.71 | 1.07 | −2.41 | 1.57 | ||||||||||||||
| rs2900180 | TRAF1 | 9 | 122746203 | CC | 425 | 6.73 | 0.98 | −2.47 | 1.61 | 0.077 | 0.730 | 0.592 | 0.04 | −0.09 | 0.17 | 0.841 | 0.02 | −0.16 | 0.20 |
| CT | 441 | 6.65 | 0.95 | −2.50 | 1.49 | ||||||||||||||
| TT | 146 | 6.70 | 1.05 | −2.41 | 1.57 | ||||||||||||||
| rs4750316 | PRKCQ | 10 | 6433266 | GG | 695 | 6.71 | 0.95 | −2.54 | 1.56 | 0.510 | 0.346 | 0.387 | 0.07 | −0.09 | 0.24 | 0.237 | 0.12 | −0.08 | 0.31 |
| GC | 283 | 6.67 | 1.01 | −2.33 | 1.50 | ||||||||||||||
| CC | 33 | 6.43 | 1.23 | −2.19 | 1.80 | ||||||||||||||
| rs1678542 | KIF5A | 12 | 56254982 | CC | 419 | 6.72 | 0.98 | −2.50 | 1.55 | 0.448 | 0.724 | 0.600 | 0.04 | −0.10 | 0.17 | 0.456 | 0.07 | −0.11 | 0.25 |
| CG | 473 | 6.65 | 0.96 | −2.44 | 1.55 | ||||||||||||||
| GG | 119 | 6.74 | 1.05 | −2.49 | 1.56 | ||||||||||||||
| rs763361 | CD226 | 18 | 65682622 | TT | 272 | 6.65 | 1.00 | −2.64 | 1.50 | 0.900 | 0.050 | 0.016 | 0.16 | 0.03 | 0.29 | 0.026 | 0.23 | 0.03 | 0.43 |
| TC | 508 | 6.69 | 0.96 | −2.45 | 1.57 | ||||||||||||||
| CC | 232 | 6.75 | 0.98 | −2.32 | 1.57 | ||||||||||||||
| rs4810485 | CD40 | 20 | 44181354 | GG | 607 | 6.68 | 0.95 | −2.50 | 1.54 | 0.048 | 0.398 | 0.221 | 0.10 | −0.06 | 0.27 | 0.325 | 0.09 | −0.09 | 0.28 |
| GT | 358 | 6.68 | 1.01 | −2.40 | 1.56 | ||||||||||||||
| TT | 35 | 6.90 | 0.97 | −2.46 | 1.65 | ||||||||||||||
Significant p values (<0.05) are shown in bold type, italic indicates p<0.10.
*
Results for the recessive model are not shown; only rs1160542 (AFF3) demonstrated association with treatment response under a recessive model (coef 0.23 (0.01, 0.45), p=0.037).
bp, base pairs; Chr, chromosome; Coef, coefficient for minor allele; DAS, disease activity score; HWE, Hardy–Weinberg equilibrium; SNP, single nucleotide polymorphism.