About

Human Genetic Variation Database (HGVD)

Data sources

The Human Genetic Variation Database (HGVD) serves as a central resource for archiving and displaying Japanese genetic variation and associations between genetic variation and gene transcription levels. The HGVD browser can be used to view allele and genotype frequencies, sample counts, coverage, and expression quantitative trait locus (eQTL) significance.

HGVD browser data tracks use the exome cohort (n = 1,209), WGS cohort (n = 3,135), or SNP-array cohort (n = 3,248); combined exome/WGS frequencies use 4,344 mutually exclusive individuals. The eQTL tracks use 300 individuals and are available only in the GRCh37/hg19 browser.

The GRCh37/hg19 data are in source coordinates, whereas the corresponding GRCh38/hg38 and T2T-CHM13 browser entries were obtained from GRCh37/hg19 by UCSC liftOver. Gene and dbSNP tracks are imported assembly-specific annotations. These values indicate maximum cohort sizes; locus-specific successfully genotyped sample counts may be smaller because missing genotypes are excluded.

Collaborating institutions

  • KU — Kyoto University
  • NCCHD — National Research Institute for Child Health and Development
  • TU — Tohoku University
  • UT — The University of Tokyo
  • YCU — Yokohama City University

Acceptance of Terms

The access to HGVD is subject to the Terms of Service described on this page. Your use of HGVD constitutes your agreement to these terms and conditions.

Data Usage

We request that any use of data obtained from HGVD be cited in publications.

Citation

  • K. Higasa et al. “Whole-genome sequencing of 3135 individuals representing the genetic diversity of the Japanese population.” Journal of Human Genetics, 2025. DOI: 10.1038/s10038-025-01430-1. Article
  • K. Higasa et al. “Human genetic variation database, a reference database of genetic variations in the Japanese population.” Journal of Human Genetics 61:547–553, 2016. DOI: 10.1038/jhg.2016.12. Article
  • M. Narahara et al. “Large-Scale East-Asian eQTL Mapping Reveals Novel Candidate Genes for LD Mapping and the Genomic Landscape of Transcriptional Effects of Sequence Variants.” PLOS ONE, 2014, 9(6):e100924. Article

Acknowledgment for Publication

This work was supported by the Research Grant (201238002A) for Intractable Diseases from the Ministry of Health, Labour and Welfare of Japan.

Terms of Service

This website is designed to disseminate exome sequencing data of the Japanese population generated through the collaborative effort. The data are provided free-of-charge, but please comply with the permission statement below. This site may also include links to other websites or databases, but we have no control over the nature or content of those sites and accept no responsibility for them.

Privacy Policy

The IP addresses of your computer and your query parameters are saved in log files, in order that we can monitor the loading of the server and improve response. Statistics of usage are collected from these log files to justify the funding of the effort.

Disclaimer

This website and all information or data accessed thereby is provided on an “AS IS” basis without warranty of any kind, either expressed or implied. Articles/publications linked to or included in this website are the opinion of the author only, and do not necessarily represent the opinion of HGVD or its clients. Although HGVD strives for all contents of this webpage to be accurate, complete and up-to-date, HGVD makes no warranty or guarantee of this.

All material contained in this website, including information, images, text, documents, graphics, products, icons, logos, and screens, is owned or licensed by HGVD unless indicated otherwise. HGVD makes no guarantee or warranty regarding the frequency or continuity of publication of articles, and specifically disclaims any liability resulting from reliance on such articles/publications.

Commercial Use of HGVD

If you intend to access and use HGVD and the Documentation for commercial purposes, including for commercial research and development work, the development and submission of information under a law which regulates the manufacture, use, or sale of drugs, which for the avoidance of doubt, includes pre-clinical testing and clinical trials, and the commercial manufacture for sale, marketing, distribution, sale, or offer for sale of products that were developed using and/or approved in view of data obtained from HGVD, please contact GenoConcierge Kyoto, Inc. (hgvd@gckyoto.com) and obtain Commercial License in advance of your Commercial Use.

Permission

The contents of HGVD are intended for educational or research purposes. We place no restrictions on the use of the data available from HGVD. You can download or copy the content and other downloadable items displayed on the website. To use the data, please follow the citation format given above.