Table 4 Top candidate SNPs selected after second stage analysis in 3-stage GWAS targeting nonsynonymous SNPs (hypoesthesia)
Model | Rank | SNP | CHR | Position | 1st stage | 2nd stage | Final stage | Combined | Genotype | Related gene | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
X 2 | P | X 2 | P | X 2 | P | Q | X 2 | P | Abnormal | Normal | ||||||
Trend | 1 | rs2839227 | 21 | 46610952 | 5.771 | 0.0163 | 8.95 | 0.0028 | 0.4962 | 0.4812 | 0.7406 | 11.63 | 0.00065 | 7/29/15 | 19/88/143 | PCNT |
Trend | 2 | rs4074536 | 1 | 116112490 | 4.724 | 0.0298 | 3.904 | 0.0482 | 0.1467 | 0.7017 | 0.7406 | 7.338 | 0.006753 | 6/24/21 | 58/135/60 | CASQ2 |
Trend | 3 | rs2296351 | 13 | 51607939 | 4.131 | 0.0421 | 4.244 | 0.0394 | 0.1096 | 0.7406 | 0.7406 | 6.061 | 0.01382 | 2/19/30 | 5/56/192 | NEK3 |
Trend | 4 | rs1339847 | 1 | 246105917 | 4.141 | 0.0419 | 4.938 | 0.0263 | 0.7541 | 0.3852 | 0.7406 | 3.974 | 0.04622 | 6/11/34 | 4/65/184 | TRIM58 |
Dominant | 1 | rs2228576 | 12 | 6327323 | 7.136 | 0.0076 | 4.904 | 0.0268 | 3.013 | 0.0826 | 0.2477 | 15.42 | 8.6E-05 | 9/35/6 | 37/108/102 | SCNN1A |
Dominant | 2 | rs2839227 | 21 | 46610952 | 7.313 | 0.0068 | 5.538 | 0.0186 | 1.604 | 0.2053 | 0.308 | 13.12 | 0.000293 | 7/29/15 | 19/88/143 | PCNT |
Dominant | 3 | rs140685 | 15 | 24771205 | 4.14 | 0.0419 | 7.867 | 0.005 | 0.7902 | 0.374 | 0.374 | 10.14 | 0.001451 | 4/13/34 | 21/125/107 | GABRA5 |
Recessive | 1 | rs1339847 | 1 | 246105917 | 11.66 | 0.0006 | 6.062 | 0.0138 | 0.2731 | 0.6013 | 0.6747 | 13.84 | 0.000199 | 6/11/34 | 4/65/184 | TRIM58 |
Recessive | 2 | rs6733871 | 2 | 80383467 | 5.553 | 0.0185 | 6.125 | 0.0133 | 2.058 | 0.1514 | 0.5334 | 12.24 | 0.000469 | 18/18/15 | 37/128/88 | LRRTM1 |
Recessive | 3 | rs913588 | 9 | 7164673 | 4.14 | 0.0419 | 6.062 | 0.0138 | 1.816 | 0.1778 | 0.5334 | 10.91 | 0.000956 | 4/11/36 | 2/55/196 | JMJD2C |
Recessive | 4 | rs1079109 | 1 | 159761664 | 3.951 | 0.0469 | 6.529 | 0.0106 | NA | NA | NA | 10.16 | 0.001432 | 3/8/38 | 1/93/156 | HSPA6 |
Recessive | 5 | rs11088981 | 21 | 43694578 | 3.991 | 0.0458 | 5.919 | 0.015 | 1.816 | 0.1778 | 0.5334 | 9.754 | 0.00179 | 3/14/34 | 1/55/195 | C21orf125 |
Recessive | 6 | rs3779234 | 7 | 35676367 | 7.646 | 0.0057 | 8.992 | 0.0027 | 0.9782 | 0.3226 | 0.6747 | 9.313 | 0.002276 | 8/14/29 | 11/116/126 | HERPUD2 |
Recessive | 7 | rs12831803 | 12 | 124127104 | 3.991 | 0.0458 | 4.344 | 0.0371 | 1.816 | 0.1778 | 0.5334 | 8.362 | 0.003831 | 4/11/36 | 3/81/169 | AACS |
Recessive | 8 | rs2032887 | 19 | 8027360 | 4.14 | 0.0419 | 4.344 | 0.0371 | NA | NA | NA | 8.362 | 0.003831 | 4/13/34 | 3/61/189 | CCL25 |
Recessive | 9 | rs12609976 | 19 | 60279634 | 3.991 | 0.0458 | 6.062 | 0.0138 | 0.7278 | 0.3936 | 0.6747 | 6.803 | 0.009103 | 3/9/39 | 2/54/197 | EPS8L1 |
Recessive | 10 | rs7173826 | 15 | 65315428 | 5.157 | 0.0232 | 5.143 | 0.0234 | 0.4055 | 0.5243 | 0.6747 | 5.549 | 0.01849 | 12/15/23 | 29/124/99 | FLJ11506 |
Recessive | 11 | rs2070180 | 3 | 122834028 | 3.991 | 0.0458 | 5.99 | 0.0144 | 0.1762 | 0.6747 | 0.6747 | 5.508 | 0.01893 | 2/5/43 | 1/47/204 | HCLS1 |
Recessive | 12 | rs10907376 | 1 | 221634426 | 3.991 | 0.0458 | 4.344 | 0.0371 | 0.1879 | 0.6647 | 0.6747 | 4.839 | 0.02782 | 3/11/37 | 3/50/200 | C1orf65 |
Recessive | 13 | rs6667999 | 1 | 223600307 | 3.999 | 0.0455 | 4.455 | 0.0348 | 0.4701 | 0.493 | 0.6747 | 3.921 | 0.04769 | 15/26/10 | 44/136/73 | DNAH14 |
Recessive | 14 | rs316019 | 6 | 160590272 | 3.991 | 0.0458 | 6.935 | 0.0085 | 0.582 | 0.4455 | 0.6747 | 3.467 | 0.0626 | 3/10/38 | 4/54/194 | SLC22A2 |