JGA-SNP dataset


JGA-SNP dataset is a frequency dataset that has aggregated 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 to be aggregated. Note that no variants with 5 alternative alleles or less are included. The GRCh37-based data was lifted over to GRCh38 by using CrossMap.

  • Version/Last updated: 2018/06/01
  • 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