Table 2.
Top thirty strongest associations among MAF >1% SNPs in MGI Freeze 3 GWASs
| rsid; chromosome position | Alleles | Allele 2 frequency | Trait description (phecode) | Cases/controls | Log odds ratio | p value | Relevant GWAS catalog citation |
|---|---|---|---|---|---|---|---|
| rs6025; chr1:169,549,811 | C/T | 0.0282 | primary hypercoagulable state (286.81) | 727/43,826 | 6.41 | 2.81e−157 | venous thromboembolism20 |
| – | – | – | hypercoagulable state (286.8) | 755/43,826 | 6.13 | 1.19e−153 | – |
| – | – | – | coagulation defects (286) | 2,693/43,826 | 2.03 | 1.80e−83 | – |
| – | – | – | other and unspecified coagulation defects (286.7) | 1,942/43,826 | 1.86 | 6.73e−50 | – |
| – | – | – | congenital deficiency of other clotting factors, including factor VII (286.12) | 94/43,826 | 11.12 | 5.24e−39 | – |
| – | – | – | other venous embolism and thrombosis (452) | 4,201/36,930 | 0.98 | 1.82e−36 | – |
| – | – | – | deep vein thrombosis (452.2) | 3,162/36,930 | 1.10 | 3.01e−34 | thrombosis21 |
| rs72660908; chr1:25,257,119 | C/G | 0.3856 | rhesus isoimmunization in pregnancy (654.2) | 145/26,348 | 2.25 | 1.40e−54 | blood protein levels22 |
| rs4148325; chr2:233,764,663 | C/T | 0.3272 | disorders of bilirubin excretion (277.4) | 321/48,830 | 1.84 | 6.00e−82 | bilirubin levels23 |
| rs143260331; chr4:110,762,205 | T/C | 0.1226 | atrial fibrillation (427.21) | 4,825/31,060 | 0.49 | 1.17e−37 | atrial fibrillation24,a |
| – | – | – | atrial fibrillation and flutter (427.2) | 4,978/31,060 | 0.48 | 2.42e−37 | atrial fibrillation/atrial flutter25,a |
| rs1800562; chr6:26,092,913 | G/A | 0.0602 | disorders of iron metabolism (275.1) | 201/47,321 | 4.33 | 1.07e−51 | hemoglobin26 |
| rs185937162; chr6:31,357,491 | T/G | 0.0428 | ankylosing spondylitis (715.2) | 190/35,793 | 4.34 | 2.92e−35 | ankylosing spondylitis27,a |
| rs2040410; chr6:32,634,921 | C/T | 0.1260 | celiac disease (557.1) | 407/37,236 | 1.63 | 5.91e−39 | celiac disease28,a |
| rs9273364; chr6:32,658,525 | T/G | 0.2769 | type 1 diabetes (250.1) | 2,266/36,631 | 0.80 | 4.23e−106 | medication use: drugs used in diabetes29 |
| – | – | – | type 2 diabetes with ophthalmic manifestations (250.23) | 1,522/36,631 | 0.54 | 1.32e−34 | – |
| rs9273368; chr6:32,658,698 | G/A | 0.2713 | type 1 diabetes with ophthalmic manifestations (250.13) | 760/36,631 | 1.41 | 2.91e−101 | latent autoimmune diabetes versus type 1 diabetes30 |
| – | – | – | type 1 diabetes with renal manifestations (250.12) | 509/36,631 | 1.55 | 4.02e−80 | – |
| – | – | – | type 1 diabetes with neurological manifestations (250.14) | 559/36,631 | 1.43 | 6.99e−76 | – |
| – | – | – | type 1 diabetes with ketoacidosis (250.11) | 205/36,631 | 1.75 | 1.23e−40 | – |
| rs1794269; chr6:32,706,117 | C/T | 0.3760 | diabetic retinopathy (250.7) | 1,544/43,849 | 0.60 | 4.53e−52 | type 2 diabetes31,a |
| – | – | – | insulin pump user (250.3) | 3,155/36,631 | 0.37 | 1.04e−39 | – |
| rs12203592; chr6:396,321 | C/T | 0.1616 | Other non-epithelial cancer of skin (172.2) | 6,627/41,896 | 0.36 | 1.83e−38 | basal cell carcinoma32 |
| – | – | – | skin cancer (172) | 8,228/41,896 | 0.32 | 1.65E-36 | – |
| – | – | – | basal cell carcinoma (172.21) | 3,509/41,896 | 0.47 | 2.36e−36 | – |
| rs113993960; chr7:117,559,590 | ATCT/A | 0.0146 | cystic fibrosis (499) | 97/51,358 | 18.90 | 9.80e−49 | lung function: FEV1/FVC33,b |
| rs28929474; chr14:94,378,610 | C/T | 0.0179 | alpha-1-antitrypsin deficiency (270.34) | 60/48,887 | 21.05 | 1.71e−52 | serum albumin level34 |
| rs1421085; chr16:53,767,042 | T/C | 0.4156 | morbid obesity (278.11) | 7,255/32,074 | 0.25 | 1.65e−36 | body mass index33 |
| rs3747207; chr22:43,928,975 | G/A | 0.2296 | other chronic non-alcoholic liver disease (571.5) | 2,973/41,006 | 0.52 | 2.95e−54 | alanine transaminase levels in high alcohol intake35 |
| – | – | – | chronic liver disease and cirrhosis (571) | 3,150/41,006 | 0.50 | 7.98e−53 | – |
The GWASs were conducted on 1,712 phecode traits with at least 20 cases in the set of 51,583 MGI samples with genetically inferred European ancestry across 51.8 million SNPs with MAFs >0.01% and imputation score Rsq >0.3. The relevant GWAS catalog citation column provides a phenotype and citation identified in the GWAS Catalog for a related trait at the indicated SNP in MGI.
a
GWAS Catalog association is within 50 kb of the indicated SNP.
b
GWAS Catalog association is within 1 Mb of the indicated SNP.