Table 1. Allele and genotype frequency of single SNP association analysis in the testing and validation datasets.
| Markers |
The testing dataset |
The validation dataset |
|||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SNP ID/bp | Allele Freq.(%) | p-value1 | Genotype Freq.(%) | p-value1 | H-WE | OR2 95%CI | Allele Freq.(%) | p-value1 | Genotype Freq.(%) | p-value1 | H-WE | OR2 95%CI | |||||||
| rs709323 | T | G | TT | GT | GG | T | G | TT | GT | GG | |||||||||
| SCZ | 53,580, 457 | 1656(74.1) | 578(25.9) | 0.073731 | 620(55.5) | 416(37.2) | 81(7.25) | 0.082293 | 0.331 | 1.12 | 2222(77.7) | 638(22.3) | 0.247525 | 868(60.7) | 486(34.0) | 76(5.31) | 0.396040 | 0.460 | 1.07 |
| CTR | 2766(76.2) | 864(23.8) | 1047(57.7) | 672(37.0) | 96(5.29) | 0.377 | 0.99–1.26 | 6769(78.8) | 1821(21.2) | 2667(62.1) | 1435(33.4) | 193(4.49) | 0.999 | 0.94–1.18 | |||||
| rs3774458 | G | A | GG | GA | AA | G | A | GG | GA | AA | |||||||||
| SCZ | 53,583, 841 | 1784(79.9) | 450(20.1) | 0.079330 | 719(64.4) | 346(31) | 52(4.66) | 0.075241 | 0.214 | 1.13 | 2369(82.8) | 491(17.2) | 0.277228 | 987(69.02) | 395(27.6) | 48(3.36) | 0.316832 | 0.276 | 1.07 |
| CTR | 2966(81.7) | 664(18.3) | 1207(66.5) | 552(30.4) | 56(3.09) | 0.458 | 0.99–1.29 | 7198(83.8) | 1392(16.2) | 3015(70.2) | 1168(27.2) | 112(2.61) | 0.930 | 0.96–1.20 | |||||
| rs1460118 | A | G | AA | AG | GG | A | G | AA | AG | GG | |||||||||
| SCZ | 53,675, 824 | 1595(71.4) | 639(28.6) | 0.061349 | 573(51.3) | 449(40.2) | 95(8.5) | 0.169869 | 0.597 | 1.12 | 2062(72.1) | 798(27.9) | 0.376238 | 748(52.31) | 566(39.6) | 116(8.11) | 0.564356 | 0.539 | 1.05 |
| CTR | 2673(73.6) | 957(26.4) | 986(54.3) | 701(38.6) | 128(7.05) | 0.823 | 0.99–1.26 | 6270(73.0) | 2320(27.0) | 2289(53.29) | 1692(39.4) | 314(7.31) | 0.956 | 0.95–1.15 | |||||
| rs3774530 | T | C | TT | TC | CC | T | C | TT | TC | CC | |||||||||
| SCZ | 53,703, 343 | 1541(69) | 693(31) | 0.080180 | 526(47.1) | 489(43.8) | 102(9.13) | 0.188375 | 0.443 | 1.09 | 1797(62.8) | 1063(37.2) | 0.178218 | 561(39.23) | 675(47.2) | 194(13.6) | 0.207921 | 0.688 | 1.07 |
| CTR | 2582(71.1) | 1048(28.9) | 917(50.5) | 748(41.2) | 150(8.26) | 0.884 | 0.98–1.24 | 5531(64.4) | 3059(35.6) | 1782(41.49) | 1967(45.8) | 546(12.7) | 0.930 | 0.98–1.17 | |||||
| rs3774601 | G | A | GG | GA | AA | G | A | GG | GA | AA | |||||||||
| SCZ | 53,788, 866 | 1723(77.1) | 511(22.9) | 0.056828 | 656(58.7) | 411(36.8) | 50(4.48) | 0.053895 | 0.152 | 1.13 | 2323(81.2) | 537(18.8) | 0.148515 | 937(65.52) | 449(31.4) | 44(3.08) | 0.207921 | 0.266 | 1.10 |
| CTR | 2720(74.9) | 910(25.1) | 1024(56.4) | 672(37) | 119(6.56) | 0.537 | 1.00–1.28 | 6855(79.8) | 1735(20.2) | 2736(63.7) | 1383(32.2) | 176(4.10) | 0.941 | 0.98–1.22 | |||||
| rs3774605 | C | T | CC | CT | TT | C | T | CC | CT | TT | |||||||||
| SCZ | 53,796, 740 | 1932(86.5) | 302(13.5) | 0.090101 | 833(74.6) | 266(23.8) | 18(1.61) | 0.156083 | 0.537 | 1.14 | 2591(90.6) | 269(9.41) | 0.178218 | 1177(82.31) | 237(16.6) | 16(1.12) | 0.158416 | 0.299 | 1.11 |
| CTR | 3081(84.9) | 549(15.1) | 1312(72.3) | 457(25.2) | 46(2.53) | 0.412 | 0.98–1.33 | 7705(89.7) | 885(10.3) | 3453(80.4) | 799(18.6) | 43(1.00) | 0.669 | 0.96–1.28 | |||||
SCZ: schizophrenia; CTR: control; CI: confidence interval; OR: odds ratio p values (p < 0.1) are in italic bold to indicate a trend of significant association.
1p-values of the normal chi-square statistics from Monte Carlo stimulation using CLUMP (T2).
2OR refers to risk allele odds ratio.