JGA-SNP dataset


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.

  1. The data user can freely present the result of the study for which data from the NBDC Human Database are used.
  2. 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.

  1. In using data, the user must take responsibility for and make judgments concerning the quality, content, and scientific validity of the data.
  2. 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.
  3. 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.

JGAIDHuman DB IDStudy titleParticipantsSample sizeData provider
JGAD000123hum0014Biobank Japan ProjectBMI research participants182,557Michiaki Kubo
JGAD000018hum0028Biobank Japan ProjectHealthy control908Michiaki Kubo
hum0082Genome-wide analysis of SNPs in Healthy JapaneseHealthy control419Katsushi Tokunaga

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 categoryDisease nameSex
NeoplasmsLung cancermale/female
Esophageal cancermale/female
Gastric cancermale/female
Colorectal cancermale/female
Liver cancermale/female
Pancreas cancermale/female
Prostate cancermale
Breast cancerfemale
Cervical cancerfemale
Uterine cancerfemale
Ovarian cancerfemale
Hematopoietic tumormale/female
Diseases of the nervous systemCerebral infarctionmale/female
Cerebral aneurysmmale/female
Diseases of the respiratory systemBronchial asthmamale/female
Pulmonary tuberculosismale/female
Chronic obstructive pulmonary diseasemale/female
Interstitial lung disease/Pulmonary fibrosismale/female
Diseases of the circulatory systemMyocardial infarctionmale/female
Unstable anginamale/female
Stable anginamale/female
Heart failuremale/female
Peripheral arterial diseasesmale/female
Hepato-Biliary-Pancreatic diseasesChronic hepatitis Bmale/female
Chronic hepatitis Cmale/female
Liver cirrhosismale/female
Diseases of the genitourinary systemNephrotic syndromemale/female
Metabolic diseasesOsteoporosismale/female
Diabetes mellitusmale/female
Endocrine diseasesGraves' diseasemale/female
Collagen diseases (connective tissue diseases)Rheumatoid arthritismale/female
AllergyHay fevermale/female
Diseases of the skin and subcutaneous tissueDrug eruptionmale/female
Atopic dermatitismale/female
Gynecological diseasesUterine fibroidfemale
Diseases of the eye and adnexaGlaucomamale/female
Oral and Maxillofacial diseasesPeriodontitismale/female