JGA-SNP dataset
Summary
The JGA-SNP dataset is a frequency dataset that aggregates variants detected from SNP-chip data in the NBDC Human Database/Japanese Genotype-phenotype Archive (JGA). All JGA data for which an approval for creating secondary data has been obtained are aggregated. In June 2024, allele and genotype frequencies aggregated by sex for 45 diseases were added by genotyping using SNP array of 182,557 individuals, performed by BioBank Japanand RIKEN. Note that variants with alternative allele counts of five or fewer are not included. The GRCh37-based data was lifted over to GRCh38 by using transanno.
- Version/Last updated: 2024/6/28
- Sample size: 183,884
- Number of detected variants (alternative alleles): 1,966,919
- Number of variants after the exclusion: 1,249,724
- Number of variants variants after the liftover from GRCh37 to GRCh38: 1,244,838
Terms of use
Rights of Data Users
The rights of data users shall conform to "5-2-1. Open Data" in "5-2. Rights of Data Users" listed in the NBDC Human Data Sharing Guidelines.
- The data user can freely present the result of the study for which data from the NBDC Human Database are used.
- The data user can freely acquire intellectual property rights based on the result of the study for which data from the NBDC Human Database are used.
Responsibilities of Data Users
Terms of "5-3-1. Open Data" in "5-3. Responsibilities of Data Users" listed in the NBDC Human Data Sharing Guidelines shall apply with modification to the responsibilities of data users. As for redistribution of data, terms for controlled-access data shall apply because this dataset was generated by processing controlled-access data.
- In using data, the user must take responsibility for and make judgments concerning the quality, content, and scientific validity of the data.
- The data user must comply with the following rules.
- The use of data is limited to the study being undertaken.
- Identification of individuals is prohibited
- Redistribution of data is prohibited.
- The data user must add the following citation while using the data in public (e.g. publishing an article).
Variant dataset aggregated from SNP-chip data in NBDC Human Database/JGA [Internet]. Kashiwa: Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems; [2018] - . JGA SNP dataset; [cited YYYY Mmm DD]. Available from: https://grch38.togovar.org/doc/datasets/jga_snp
Included controlled-access datasets
By specifying the JGAID, you can apply for data use to the NBDC Human database.
JGAID | Human DB ID | Study title | Participants | Sample size | Data provider |
---|---|---|---|---|---|
JGAD000123 | hum0014 | Biobank Japan Project | BMI research participants | 182,557 | Michiaki Kubo |
JGAD000018 | hum0028 | Biobank Japan Project | Healthy control | 908 | Michiaki Kubo |
JGAD000130 JGAD000131 | hum0082 | Genome-wide analysis of SNPs in Healthy Japanese | Healthy control | 419 | Katsushi Tokunaga |
Total | 183,884 |
List of 45 diseases included in JGAD000123 from BioBank Japan and RIKEN
We published the frequencies aggregated by disease and sex for the dataset JGAD000123 in June 2024. In some cases, multiple disease names were assigned to the same sample. Please see the publication below for details about the samples. By using the “Alternative allele frequency/count” in the Advanced search, you can search for variants based on the frequencies aggregated by disease and sex.
Hirata M, Kamatani Y, Nagai A, et al. Cross-sectional analysis of BioBank Japan clinical data: A large cohort of 200,000 patients with 47 common diseases. J Epidemiol. 2017;27(3S):S9-S21. doi:10.1016/j.je.2016.12.003.
Disease category | Disease name | Sex |
---|---|---|
Neoplasms | Lung cancer | male/female |
Esophageal cancer | male/female | |
Gastric cancer | male/female | |
Colorectal cancer | male/female | |
Liver cancer | male/female | |
Pancreas cancer | male/female | |
Gallbladder/Cholangiocarcinoma | male/female | |
Prostate cancer | male | |
Breast cancer | female | |
Cervical cancer | female | |
Uterine cancer | female | |
Ovarian cancer | female | |
Hematopoietic tumor | male/female | |
Diseases of the nervous system | Cerebral infarction | male/female |
Cerebral aneurysm | male/female | |
Epilepsy | male/female | |
Diseases of the respiratory system | Bronchial asthma | male/female |
Pulmonary tuberculosis | male/female | |
Chronic obstructive pulmonary disease | male/female | |
Interstitial lung disease/Pulmonary fibrosis | male/female | |
Diseases of the circulatory system | Myocardial infarction | male/female |
Unstable angina | male/female | |
Stable angina | male/female | |
Arrhythmia | male/female | |
Heart failure | male/female | |
Peripheral arterial diseases | male/female | |
Hepato-Biliary-Pancreatic diseases | Chronic hepatitis B | male/female |
Chronic hepatitis C | male/female | |
Liver cirrhosis | male/female | |
Diseases of the genitourinary system | Nephrotic syndrome | male/female |
Urolithiasis | male/female | |
Metabolic diseases | Osteoporosis | male/female |
Diabetes mellitus | male/female | |
Dyslipidemia | male/female | |
Endocrine diseases | Graves' disease | male/female |
Collagen diseases (connective tissue diseases) | Rheumatoid arthritis | male/female |
Allergy | Hay fever | male/female |
Diseases of the skin and subcutaneous tissue | Drug eruption | male/female |
Atopic dermatitis | male/female | |
Keloid | male/female | |
Gynecological diseases | Uterine fibroid | female |
Endometriosis | female | |
Diseases of the eye and adnexa | Glaucoma | male/female |
Cataract | male/female | |
Oral and Maxillofacial diseases | Periodontitis | male/female |