Table 1.
Summary of phecode traits and GWAS results in European MGI participants
| Phecode category | Total phecode traits | Analyzed traits (≥60 cases) | Traits with ≥1 GWS loci (MAF >1%) | Number of GWS loci (MAF >1%) | Strongest association (MAF >1%) |
|---|---|---|---|---|---|
| Circulatory system | 171 | 160 | 108 (43) | 200 (72) | atrial fibrillation (427.21), p = 1.2e−37, chr4:110,762,205 |
| Congenital anomalies | 56 | 44 | 18 (3) | 36 (3) | genitourinary congenital anomalies (751), p = 4.0e−09, chr2:161,318,326 |
| Dermatologic | 95 | 77 | 53 (17) | 93 (22) | psoriasis vulgaris (696.41), p = 4.7e−28, chr6:31,274,954 |
| Digestive | 162 | 149 | 95 (39) | 198 (59) | other chronic non-alcoholic liver disease (571.5), p = 3.0e−54, chr22:43,928,975 |
| Endocrine/metabolic | 169 | 129 | 92 (65) | 277 (180) | type 1 diabetes (250.1), p = 4.2e−106, chr6:32,658,525 |
| Genitourinary | 173 | 157 | 101 (25) | 191 (39) | nephritis and nephropathy in diseases classified elsewhere (580.31), p = 1.4e−19, chr6:32,706,117 |
| Hematopoietic | 62 | 45 | 32 (16) | 65 (26) | primary hypercoagulable state (286.81), p = 2.8e−157, chr1:169,549,811 |
| Infectious diseases | 69 | 54 | 28 (8) | 37 (8) | aspergillosis (117.4), p = 4.3e−17, chr7:117,559,590 |
| Injuries and poisonings | 122 | 93 | 49 (5) | 79 (6) | salicylates causing adverse effects in therapeutic use (965.3), p = 2.4e−10, chr6:33,091,097 |
| Mental disorders | 76 | 63 | 39 (11) | 64 (12) | dementias (290.1), p = 2.1e−18, chr19:44,908,684 |
| Musculoskeletal | 132 | 114 | 71 (19) | 121 (20) | ankylosing spondylitis (715.2), p = 2.9e−35, 6:31,357,491 |
| Neoplasms | 141 | 129 | 76 (29) | 194 (85) | other non-epithelial cancer of skin (172.2), p = 1.8e−38, chr6:396,321 |
| Neurological | 85 | 74 | 50 (11) | 79 (14) | restless legs syndrome (327.71), p = 6.8e−29, chr2:66,523,432 |
| Pregnancy complications | 46 | 28 | 18 (7) | 23 (7) | rhesus isoimmunization in pregnancy (654.2), p = 1.4e−54, chr1:25,257,119 |
| Respiratory | 85 | 78 | 57 (22) | 96 (26) | cystic fibrosis (499), p = 9.8e−49, chr7:117,559,590 |
| sense organs | 127 | 112 | 65 (18) | 105 (25) | Fuchs’ dystrophy (364.51), p = 2.0e−31, chr18:55,543,071 |
| Symptoms | 46 | 41 | 25 (2) | 43 (2) | fever of unknown origin (783), p = 2.9e−08, chr7:37,808,912 |
| Total | 1,817 | 1,547 | 977 (340) | 1,901 (606) |
We report results for phecode traits with at least sixty cases. The strongest association column contains the phecode trait name (numerical phecode), p value, and chromosomal location for the association with smallest p value in each phecode category. A threshold of p = 5e−8 was used for genome-wide significance (GWS).