Table 1.
Effects of the SNPs on DR in stage 1 samples.
| Chr. | SNP | Position (Build 38) | Gene | Minor/major allele | Risk allele | Controls vs DR only | DKD only vs DKD&DR | Meta-analysis | |||
|---|---|---|---|---|---|---|---|---|---|---|---|
| OR (95% CI) | P a | OR (95% CI) | P a | OR (95% CI) | P a | ||||||
| 1 | rs2641348 | 119895261 | ADAM30 | C/T | C | 1.200 (0.586, 2.455) | 0.62 | 1.020 (0.492, 2.116) | 0.96 | 1.108 (0.665, 1.847) | 0.69 |
| 1 | rs10923931 | 119975336 | NOTCH2 | T/G | T | 1.132 (0.562, 2.283) | 0.73 | 0.918 (0.438, 1.924) | 0.82 | 1.025 (0.616, 1.705) | 0.92 |
| 1 | rs340874 | 213985913 | PROX1 | G/A | G | 1.162 (0.878, 1.540) | 0.29 | 0.946 (0.726, 1.232) | 0.68 | 1.042 (0.859, 1.263) | 0.68 |
| 2 | rs7578597 | 43505684 | THADA | C/T | C | 1.060 (0.162, 6.924) | 0.95 | 0.971 (0.260, 3.625) | 0.97 | 1.000 (0.340, 2.938) | 1.00 |
| 2 | rs243021 | 60357684 | LOC105374756 | C/T | T | 0.978 (0.722, 1.324) | 0.89 | 1.009 (0.766, 1.329) | 0.95 | 0.995 (0.811, 1.220) | 0.96 |
| 2 | rs7593730 | 160314943 | RBMS1 | T/C | C | 0.795 (0.538, 1.173) | 0.25 | 0.909 (0.640, 1.292) | 0.60 | 0.856 (0.659, 1.111) | 0.24 |
| 2 | rs3923113 | 164645339 | GRB14 | G/T | G | 0.921 (0.563, 1.506) | 0.74 | 1.489 (1.026, 2.160) | 0.0361 | 1.250 (0.929, 1.682) | 0.14 |
| 2 | rs13389219 | 164672366 | LOC101929615 | T/C | T | 0.854 (0.504, 1.449) | 0.56 | 1.316 (0.822, 2.107) | 0.25 | 1.087 (0.765, 1.545) | 0.64 |
| 2 | rs16856187 | 168913876 | G6PC2 | C/A | A | 0.941 (0.687, 1.290) | 0.71 | 0.874 (0.646, 1.182) | 0.38 | 0.906 (0.728, 1.126) | 0.37 |
| 2 | rs7578326 | 226155937 | LOC646736 | G/A | A | 0.946 (0.645, 1.385) | 0.77 | 0.810 (0.548, 1.197) | 0.29 | 0.877 (0.667, 1.152) | 0.34 |
| 2 | rs2943641 | 226229029 | LOC646736 | T/C | T | 1.146 (0.613, 2.146) | 0.67 | 0.939 (0.546, 1.617) | 0.82 | 1.023 (0.679, 1.542) | 0.91 |
| 3 | rs1801282 | 12351626 | PPARG | G/C | G | 0.921 (0.493, 1.719) | 0.80 | 2.048 (1.085, 3.863) | 0.0269 | 1.364 (0.874, 2.129) | 0.17 |
| 3 | rs7612463 | 23294959 | UBE2E2 | A/C | C | 0.915 (0.648, 1.292) | 0.61 | 0.937 (0.676, 1.300) | 0.70 | 0.927 (0.731, 1.175) | 0.53 |
| 3 | rs831571 | 64062621 | PSMD6 | T/C | C | 0.895 (0.659, 1.215) | 0.48 | 1.038 (0.797, 1.352) | 0.78 | 0.974 (0.798, 1.190) | 0.80 |
| 3 | rs4607103 | 64726228 | ADAMTS9-AS2 | T/C | C | 0.719 (0.534, 0.967) | 0.0292 | 0.771 (0.582, 1.021) | 0.07 | 0.746 (0.608, 0.915) | 0.0048 |
| 3 | rs4402960 | 185793899 | IGF2BP2 | T/G | G | 1.000 (0.728, 1.372) | 1.00 | 0.927 (0.694, 1.237) | 0.61 | 0.959 (0.775, 1.187) | 0.70 |
| 3 | rs7651090 | 185795604 | IGF2BP2 | G/A | A | 1.060 (0.770, 1.461) | 0.72 | 0.922 (0.687, 1.239) | 0.59 | 0.983 (0.791, 1.221) | 0.88 |
| 3 | rs16861329 | 186948673 | ST64GAL1 | T/C | C | 0.980 (0.688, 1.397) | 0.91 | 0.964 (0.676, 1.373) | 0.84 | 0.972 (0.757, 1.248) | 0.82 |
| 4 | rs6815464 | 1316113 | MAEA | G/C | C | 0.918 (0.683, 1.233) | 0.57 | 1.046 (0.808, 1.355) | 0.73 | 0.988 (0.814, 1.201) | 0.91 |
| 4 | rs10010131 | 6291188 | WFS1 | A/G | A | 1.910 (0.930, 3.923) | 0.08 | 1.448 (0.779, 2.692) | 0.24 | 1.629 (1.019, 2.606) | 0.0416 |
| 5 | rs459193 | 56510924 | C5orf67 | T/C | C | 0.899 (0.679, 1.192) | 0.46 | 0.975 (0.745, 1.278) | 0.86 | 0.938 (0.772, 1.140) | 0.52 |
| 5 | rs4457053 | 77129124 | ZBED3-AS1 | G/A | A | 0.837 (0.460, 1.524) | 0.56 | 1.087 (0.595, 1.986) | 0.79 | 0.953 (0.623, 1.458) | 0.82 |
| 6 | rs7756992 | 20679478 | CDKAL1 | A/G | G | 0.697 (0.522, 0.931) | 0.0145 | 0.707 (0.547, 0.913) | 0.0079 | 0.703 (0.580, 0.851) | 0.0003 |
| 6 | rs9470794 | 38139068 | ZFAND3 | C/T | C | 1.174 (0.873, 1.577) | 0.29 | 1.007 (0.765, 1.326) | 0.96 | 1.081 (0.884, 1.322) | 0.45 |
| 6 | rs1535500 | 39316274 | KCNK16 | T/G | T | 1.239 (0.936, 1.640) | 0.13 | 1.075 (0.833, 1.386) | 0.58 | 1.146 (0.949, 1.384) | 0.16 |
| 7 | rs2191349 | 15024684 | GTF3AP5 | G/T | G | 1.261 (0.952, 1.671) | 0.11 | 0.977 (0.750, 1.273) | 0.87 | 1.101 (0.908, 1.335) | 0.33 |
| 7 | rs864745 | 28140937 | JAZF1 | G/A | G | 1.209 (0.856, 1.709) | 0.28 | 0.992 (0.714, 1.378) | 0.96 | 1.090 (0.859, 1.383) | 0.48 |
| 7 | rs1799884 | 44189469 | GCK | A/G | A | 1.276 (0.920, 1.770) | 0.15 | 1.034 (0.763, 1.400) | 0.83 | 1.139 (0.912, 1.423) | 0.25 |
| 7 | rs917793 | 44206254 | YKT6 | A/T | A | 1.190 (0.856, 1.654) | 0.30 | 1.082 (0.800, 1.463) | 0.61 | 1.130 (0.905, 1.412) | 0.28 |
| 7 | rs6467136 | 127524904 | LOC105375490 | A/G | G | 0.847 (0.585, 1.224) | 0.38 | 0.791 (0.559, 1.117) | 0.18 | 0.816 (0.634, 1.050) | 0.11 |
| 7 | rs10229583 | 127606849 | PAX4 | A/G | G | 0.958 (0.654, 1.404) | 0.83 | 0.908 (0.639, 1.291) | 0.59 | 0.931 (0.718, 1.206) | 0.59 |
| 7 | rs791595 | 128222749 | LOC101928423 | A/G | A | 1.166 (0.800, 1.699) | 0.43 | 1.270 (0.866, 1.863) | 0.22 | 1.216 (0.930, 1.591) | 0.15 |
| 7 | rs972283 | 130782095 | LOC105375508 | A/G | G | 1.077 (0.782, 1.483) | 0.65 | 0.838 (0.630, 1.115) | 0.23 | 0.937 (0.757, 1.159) | 0.55 |
| 8 | rs516946 | 41661730 | ANK1 | A/G | A | 1.175 (0.731, 1.891) | 0.51 | 1.302 (0.874, 1.941) | 0.20 | 1.248 (0.919, 1.694) | 0.16 |
| 8 | rs515071 | 41661944 | ANK1 | T/C | T | 1.347 (0.893, 2.033) | 0.16 | 1.049 (0.732, 1.504) | 0.79 | 1.169 (0.892, 1.533) | 0.26 |
| 8 | rs896854 | 94948283 | TP53INP1 | A/G | G | 0.743 (0.546, 1.011) | 0.06 | 0.926 (0.703, 1.219) | 0.58 | 0.840 (0.684, 1.031) | 0.10 |
| 8 | rs13266634 | 117172544 | SLC30A8 | T/C | T | 0.934 (0.698, 1.249) | 0.65 | 1.250 (0.954, 1.637) | 0.11 | 1.092 (0.896, 1.331) | 0.38 |
| 9 | rs7041847 | 4287466 | GLIS3 | A/G | G | 1.199 (0.902, 1.595) | 0.21 | 0.858 (0.661, 1.113) | 0.25 | 0.999 (0.824, 1.211) | 0.99 |
| 9 | rs17584499 | 8879118 | PTPRD | T/C | T | 1.084 (0.674, 1.745) | 0.74 | 1.013 (0.656, 1.565) | 0.95 | 1.045 (0.758, 1.440) | 0.79 |
| 9 | rs10811661 | 22134095 | CDKN2A/B | C/T | C | 1.006 (0.754, 1.342) | 0.97 | 1.217 (0.929, 1.594) | 0.15 | 1.113 (0.914, 1.356) | 0.29 |
| 9 | rs13292136 | 79337213 | CHCHD2P9 | T/C | C | 1.150 (0.671, 1.972) | 0.61 | 0.794 (0.485, 1.300) | 0.36 | 0.940 (0.653, 1.353) | 0.74 |
| 9 | rs2796441 | 81694033 | LOC101927502 | C/T | C | 1.622 (1.209, 2.176) | 0.0013 | 1.025 (0.794, 1.322) | 0.85 | 1.282 (0.817, 2.009) | 0.28 |
| 9 | rs11787792 | 136357696 | GPSM1 | G/A | G | 0.708 (0.355, 1.412) | 0.33 | 1.662 (0.772, 3.579) | 0.19 | 1.037 (0.621, 1.733) | 0.89 |
| 10 | rs10906115 | 12272998 | CDC123 | G/A | A | 0.843 (0.624, 1.138) | 0.26 | 0.874 (0.667, 1.145) | 0.33 | 0.860 (0.704, 1.051) | 0.14 |
| 10 | rs12779790 | 12286011 | CDC123 | G/A | G | 0.877 (0.612, 1.255) | 0.47 | 1.163 (0.827, 1.635) | 0.39 | 1.017 (0.794, 1.302) | 0.89 |
| 10 | rs1802295 | 69171718 | VPS26A | T/C | C | 0.842 (0.535, 1.324) | 0.46 | 0.520 (0.319, 0.847) | 0.0086 | 0.673 (0.483, 0.939) | 0.0197 |
| 10 | rs12571751 | 79182874 | ZMIZ1 | G/A | G | 1.274 (0.962, 1.687) | 0.09 | 0.943 (0.731, 1.217) | 0.65 | 1.080 (0.894, 1.305) | 0.42 |
| 10 | rs1111875 | 92703125 | IDE-KIF11-HHEX | C/T | T | 0.720 (0.523, 0.991) | 0.0439 | 0.880 (0.669, 1.157) | 0.36 | 0.808 (0.656, 0.995) | 0.0448 |
| 10 | rs7903146 | 112998590 | TCF7L2 | T/C | C | 0.820 (0.431, 1.563) | 0.55 | 0.924 (0.469, 1.818) | 0.82 | 0.868 (0.544, 1.384) | 0.55 |
| 10 | rs10886471 | 119389891 | GRK5 | T/C | C | 0.766 (0.543, 1.080) | 0.13 | 0.829 (0.605, 1.137) | 0.24 | 0.800 (0.634, 1.009) | 0.06 |
| 11 | rs231362 | 2670241 | KCNQ1 | T/C | T | 1.281 (0.767, 2.140) | 0.34 | 0.964 (0.621, 1.496) | 0.87 | 1.087 (0.779, 1.518) | 0.62 |
| 11 | rs2237892 | 2818521 | KCNQ1 | T/C | C | 0.794 (0.575, 1.096) | 0.16 | 0.975 (0.719, 1.322) | 0.87 | 0.885 (0.709, 1.104) | 0.28 |
| 11 | rs5219 | 17388025 | KCNJ11 | T/C | C | 0.936 (0.701, 1.249) | 0.65 | 0.977 (0.740, 1.288) | 0.87 | 0.957 (0.783, 1.168) | 0.66 |
| 11 | rs10751301 | 78983593 | TENM4 | C/G | G | 0.936 (0.670, 1.308) | 0.70 | 0.934 (0.675, 1.292) | 0.68 | 0.935 (0.741, 1.180) | 0.57 |
| 11 | rs1387153 | 92940662 | MTNR1B | T/C | T | 1.057 (0.799, 1.398) | 0.70 | 1.214 (0.929, 1.587) | 0.15 | 1.136 (0.936, 1.379) | 0.20 |
| 12 | rs10842994 | 27812217 | LOC105369709 | T/C | C | 1.210 (0.829, 1.765) | 0.32 | 0.803 (0.568, 1.135) | 0.21 | 0.968 (0.750, 1.250) | 0.80 |
| 12 | rs1531343 | 65781114 | RPSAP52 | C/G | G | 0.802 (0.554, 1.163) | 0.24 | 0.856 (0.591, 1.241) | 0.41 | 0.829 (0.637, 1.078) | 0.16 |
| 12 | rs7961581 | 71269322 | LOC105369832 | C/T | T | 1.389 (0.972, 1.984) | 0.07 | 0.698 (0.500, 0.973) | 0.034 | 0.981 (0.500, 1.927) | 0.96 |
| 13 | rs9552911 | 23290518 | SGCG | A/G | G | 0.925 (0.656, 1.305) | 0.66 | 1.031 (0.763, 1.392) | 0.84 | 0.984 (0.784, 1.234) | 0.89 |
| 13 | rs1359790 | 80143021 | LOC105370275 | T/C | T | 0.984 (0.710, 1.364) | 0.92 | 1.110 (0.831, 1.482) | 0.48 | 1.053 (0.848, 1.307) | 0.64 |
| 15 | rs7403531 | 38530704 | RASGRP1 | T/C | T | 1.211 (0.912, 1.607) | 0.19 | 1.174 (0.893, 1.544) | 0.25 | 1.192 (0.979, 1.451) | 0.08 |
| 15 | rs7172432 | 62104190 | NPM1P47 | G/A | G | 1.074 (0.797, 1.449) | 0.64 | 1.269 (0.956, 1.684) | 0.10 | 1.173 (0.955, 1.441) | 0.13 |
| 15 | rs1436955 | 62112183 | NPM1P47 | A/G | A | 0.929 (0.661, 1.304) | 0.67 | 1.226 (0.903, 1.665) | 0.19 | 1.082 (0.862, 1.359) | 0.49 |
| 15 | rs7178572 | 77454848 | HMG20A | G/A | G | 1.061 (0.793, 1.419) | 0.69 | 1.020 (0.774, 1.344) | 0.89 | 1.039 (0.851, 1.270) | 0.71 |
| 15 | rs7177055 | 77540420 | LOC101929457 | A/G | A | 1.019 (0.758, 1.369) | 0.90 | 1.024 (0.780, 1.344) | 0.86 | 1.022 (0.836, 1.248) | 0.83 |
| 15 | rs11634397 | 80139880 | ZFAND6 | G/A | G | 1.125 (0.685, 1.847) | 0.64 | 1.552 (1.032, 2.333) | 0.0346 | 1.363 (0.995, 1.868) | 0.05 |
| 15 | rs2028299 | 89831025 | AP3S2 | C/A | A | 0.936 (0.667, 1.314) | 0.70 | 0.925 (0.678, 1.262) | 0.62 | 0.930 (0.740, 1.170) | 0.54 |
| 15 | rs8042680 | 90978107 | PRC1 | C/A | A | 0.342 (0.074, 1.585) | 0.17 | 1.265 (0.197, 8.137) | 0.80 | 0.580 (0.178, 1.896) | 0.37 |
| 16 | rs8050136 | 53782363 | FTO | A/C | C | 1.113 (0.745, 1.662) | 0.60 | 0.866 (0.599, 1.252) | 0.45 | 0.972 (0.741, 1.274) | 0.83 |
| 16 | rs7202877 | 75213347 | CTRB1 | G/T | T | 0.928 (0.652, 1.321) | 0.68 | 0.897 (0.661, 1.218) | 0.49 | 0.910 (0.723, 1.147) | 0.43 |
| 16 | rs17797882 | 79373021 | MAF | T/C | T | 1.036 (0.716, 1.499) | 0.85 | 1.145 (0.836, 1.568) | 0.40 | 1.098 (0.864, 1.395) | 0.44 |
| 16 | rs16955379 | 81455768 | CMIP | T/C | C | 0.947 (0.684, 1.311) | 0.74 | 0.905 (0.662, 1.237) | 0.53 | 0.925 (0.738, 1.159) | 0.50 |
| 17 | rs391300 | 2312964 | SRR | A/G | A | 0.893 (0.651, 1.225) | 0.48 | 1.206 (0.910, 1.599) | 0.19 | 1.056 (0.855, 1.303) | 0.61 |
| 17 | rs312457 | 7037074 | SLC16A13 | C/T | C | 1.228 (0.810, 1.861) | 0.33 | 1.001 (0.715, 1.403) | 0.99 | 1.086 (0.835, 1.411) | 0.54 |
| 17 | rs13342232 | 7042621 | SLC16A11 | G/A | G | 1.262 (0.828, 1.924) | 0.28 | 1.202 (0.850, 1.701) | 0.30 | 1.226 (0.938, 1.602) | 0.14 |
| 17 | rs4430796 | 37738049 | HNF1B | G/A | A | 0.855 (0.641, 1.141) | 0.29 | 1.089 (0.836, 1.417) | 0.53 | 0.976 (0.803, 1.185) | 0.80 |
| 18 | rs12970134 | 60217517 | LOC342784 | A/G | A | 1.095 (0.782, 1.532) | 0.60 | 1.301 (0.963, 1.757) | 0.09 | 1.205 (0.963, 1.508) | 0.10 |
| 19 | rs10401969 | 19296909 | SUGP1 | C/T | C | 1.064 (0.661, 1.713) | 0.80 | 0.987 (0.641, 1.518) | 0.95 | 1.021 (0.742, 1.405) | 0.90 |
| 19 | rs3786897 | 33402102 | PEPD | G/A | G | 1.094 (0.825, 1.452) | 0.53 | 1.062 (0.817, 1.381) | 0.65 | 1.077 (0.888, 1.305) | 0.45 |
| 20 | rs6017317 | 44318326 | FITM2 | G/T | G | 0.873 (0.654, 1.164) | 0.35 | 1.138 (0.879, 1.473) | 0.33 | 1.011 (0.834, 1.225) | 0.91 |
| 20 | rs4812829 | 44360627 | HNF4A | A/G | G | 0.790 (0.595, 1.049) | 0.10 | 0.903 (0.701, 1.162) | 0.43 | 0.851 (0.705, 1.028) | 0.09 |
| X | rs5945326 | 153634467 | DUSP9 | G/A | G | 1.123 (0.792, 1.593) | 0.51 | 1.209 (0.877, 1.667) | 0.25 | 1.169 (0.923, 1.480) | 0.20 |
DKD = diabetic kidney disease; DR = diabetic retinopathy.
P values < 0.05 are shown in bold.
aAdjusted for duration of diabetes, HbA1c, systolic blood pressure, diastolic blood pressure, body mass index under an additive model.
The OR with 95% CI shown is for the minor allele.