Table 2. Association results for top PheWAS signals (P<1.0 × 104) in the discovery set and validation set.
| Discovery set | Validation set | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SNP | Type | Gene | ICD9 | Description | P-value | OR (95% CI) | Cases (MAF) | Controls (MAF) | P-value | OR (95% CI) | Cases (MAF) | Controls (MAF) |
| rs10491178 | G | ABCA10 | 388 | Other disorders of ear | 4.0E−5 | 0.50 (0.36–0.69) | 786 (0.028) | 2717 (0.054) | 0.42 | 0.92 (0.76–1.1) | 1353 (0.046) | 7733 (0.05) |
| rs10838851 | G | OR4 × 1 | 617.3 | Endometriosis of pelvic peritoneum | 8.1E−5 | 2.4 (1.5–3.6) | 44 (0.42) | 4191 (0.24) | 0.64 | 1.1 (0.85–1.3) | 236 (0.24) | 10 404 (0.24) |
| rs12520799 | G | C5orf20 | 295.62 | Chronic schizophrenic disorders | 6.7E−5 | 11 (2.5–47) | 10 (0.90) | 4224 (0.45) | 0.80 | 1.0 (0.60–1.7) | 28 (0.46) | 10 612 (0.46) |
| rs12568784 | G | FLG2 | 722.7 | Intervertebral disc disorder with myelopathy | 5.2E−5 | 4.9 (2.3–11) | 13 (0.46) | 4222 (0.15) | 0.08 | 1.2 (0.54–2.8) | 19 (0.18) | 10 621 (0.16) |
| rs1667366 | L | ZNF568 | 716.95 | Unspecified arthropathy of pelvic region and thigh | 7.5E−5 | 1.8 (1.4–2.5) | 94 (0.64) | 4141 (0.49) | 0.30 | 1.2 (0.86–1.6) | 81 (0.53) | 10 559 (0.49) |
| rs1790218 | G | SLC22 A10 | 447.7 | Aortic ectasia | 7.9E−5 | 1.4 (0.68–3.0) | 14 (0.50) | 4221 (0.41) | 0.50 | 0.74 (0.44–1.2) | 32 (0.34) | 10 608 (0.41) |
| rs1861050 | G | CC2D2A | 656 | Fetal and placental problems affecting management of mother | 8.4E−5 | 0.78 (0.29–2.1) | 61 (0.033) | 4167 (0.042) | 0.13 | 1.2 (0.78–1.8) | 260 (0.048) | 9856 (0.041) |
| rs2176186 | G | C2orf83 | 719.16 | Hemarthrosis, lower leg | 4.0E−5 | 2.1 (1.2–3.4) | 30 (0.47) | 4205 (0.30) | 0.11 | 1.4 (0.91–2.3) | 40 (0.39) | 10 599 (0.31) |
| rs2176186 | G | C2orf83 | 211.3 | Benign neoplasm of colon | 6.2E−5 | 2.3 (1.5–3.4) | 49 (0.49) | 4186 (0.30) | 0.53 | 0.76 (0.38–1.5) | 22 (0.25) | 10 617 (0.31) |
| rs3731608 | G | DBI | V58.6 | Current long-term drug use | 3.2E−6 | 0.70 (0.60–0.82) | 3725 (0.20) | 510 (0.26) | 0.75 | 0.99 (0.93–1.1) | 6671 (0.20) | 3949 (0.20) |
| rs3743503 | L | CENPN | 389.22 | Hearing loss-bilateral mixed | 7.1E−5 | 0.91 (0.45–1.8) | 38 (0.12) | 4197 (0.13) | 0.12 | 1.093 (0.63–1.9) | 56 (0.13) | 10 582 (0.12) |
| rs41463245 | G | CCL26 | 530 | Diseases of esophagus | 8.8E−5 | 9.6 (4.0–23) | 30 (0.10) | 4200 (0.011) | 1.0 | 0.50 (0.07–3.6) | 68 (0.0070) | 10 569 (0.015) |
| rs4148974 | G | NDUFV3 | 438.84 | Other late effects of cerebrovascular disease, ataxia | 9.4E−5 | 5.3 (2.3–13) | 14 (0.25) | 4221 (0.059) | 1.0 | 0.88 (0.12–6.6) | 10 (0.050) | 10 626 (0.057) |
| rs5065 | L | NPPA | 781.8 | Neurologic neglect syndrome | 2.4E−5 | 4.6 (1.8–12) | 9 (0.44) | 4226 (0.15) | 0.26 | 1.5 (0.63–3.8) | 15 (0.20) | 10 625 (0.14) |
| rs5744168 | G | TLR5 | V13.09 | Personal history of other specified urinary system disorders | 7.7E−5 | 3.0 (1.7–5.3) | 47 (0.16) | 4177 (0.059) | 0.16 | 1.6 (0.88–2.9) | 61 (0.098) | 10 575 (0.064) |
| rs6024911 | L | GCNT7 | 363.4 | Choroidal degenerations | 4.4E−5 | 1.7 (1.3–2.1) | 161 (0.31) | 4070 (0.22) | 0.63 | 0.92 (0.70–1.2) | 173 (0.20) | 10 466 (0.21) |
| rs650825 | G | OPRM1 | 553 | Other hernia of abdominal cavity without mention of obstruction or gangrene | 5.3E−5 | 1.3 (1.1–1.5) | 826 (0.29) | 3013 (0.24) | 0.42 | 0.96 (0.86–1.1) | 1097 (0.24) | 8930 (0.25) |
| rs677830 | G | OPRM1 | 553 | Other hernia of abdominal cavity without mention of obstruction or gangrene | 5.3E−5 | 1.3 (1.1–1.5) | 826 (0.29) | 3013 (0.24) | 0.42 | 0.95 (0.86–1.1) | 1097 (0.24) | 8930 (0.25) |
| rs745961 | L | CEP89 | V05.3 | Need for prophylactic vaccination and inoculation against viral hepatitis | 7.0E−5 | 1.3 (1.1–1.5) | 490 (0.41) | 3744 (0.35) | 0.67 | 1.0 (0.94–1.1) | 1409 (0.36) | 9230 (0.36) |
| rs7485773 | G | ACSM4 | 562.12 | Diverticulitis of colon with hemorrhage | 3.1E−5 | 4.6 (2.5–8.4) | 39 (0.17) | 4194 (0.042) | 0.67 | 1.3 (0.31–5.4) | 19 (0.053) | 10 621 (0.041) |
| rs79448530 | G | C11orf40 | 483 | Pneumonia due to other specified organism | 7.5E−5 | 5.3 (2.6–11) | 21 (0.24) | 4213 (0.056) | 0.27 | 1.7 (0.68–4.3) | 28 (0.089) | 10 612 (0.054) |
| rs850763 | G | SLC5A9 | V15.09 | Other allergy, other than to medicinal agents | 1.7E−5 | 1.8 (1.4–2.3) | 153 (0.27) | 4081 (0.17) | 0.95 | 0.99 (0.81–1.2) | 312 (0.17) | 10 328 (0.17) |
| rs935706 | L | ZNF568 | 716.95 | Unspecified arthropathy of pelvic region and thigh | 7.5E−5 | 1.8 (1.4–2.5) | 94 (0.64) | 4141 (0.49) | 0.30 | 1.2 (0.86–1.6) | 81 (0.53) | 10 558 (0.49) |
| rs9427397 | G | FCGR2A | 531.7 | Chronic gastric ulcer without mention of hemorrhage or perforation | 5.7E−5 | 2.8 (1.8–4.5) | 43 (0.29) | 4190 (0.13) | 0.84 | 1.0 (0.52–2.0) | 40 (0.13) | 10 600 (0.12) |
| rs9973206 | G | USP29 | 562.11 | Diverticulitis of colon (without mention of hemorrhage) | 5.7E−5 | 1.5 (1.2–1.7) | 359 (0.24) | 3875 (0.18) | 0.61 | 0.95 (0.76–1.2) | 278 (0.17) | 10 223 (0.18) |
Abbreviations: CI, confidence interval; G, stop-gain; ICD9, International Classification of Disease, version 9; L, stop-loss; MAF, mean allelic frequency; OR, allelic odds ratio; SNP, single-nucleotide polymorphism.