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

Included controlled-access datasets

By specifying the JGAID, you can apply for data use to the NBDC Human database.

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.