Human Genetic Variation Database (HGVD)
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About HGVD
HGVD (Human Genetic Variation Database)は、2013年に国内で初めて公開された日本人のゲノム情報データベースです。
このデータベースは京都大学医学研究科附属ゲノム医学センターを研究代表者とする厚生労働省難病実用化研究により2013年に構築され、予算措置が終了したあとは、同センターで獲得したAMED委託研究費などで維持・管理されておりました。HGVDは構築されて以来、アクセス回数約380万回、データダウンロード回数7,700回という実績を上げており、また発表論文は220回の引用があり、医学・生命科学のコミュニティに対し極めて大きな貢献をしてまいりました。
2020年度でAMED委託研究費は終了しましたが、HGVDを長期にわたって運営しさらに発展させることは、研究者コミュニティに対する責務であると考え、HGVDの権利をゲノム医学センターの研究成果を活用したスピンオフベンチャーであるジェノコンシェルジュ京都株式会社に移管し、弊社がHGVDの継続的なアップデートおよびメンテナンスの業務を承継しました。
このデータベースには、日本人の遺伝的背景を網羅する約4200名の検体群からゲノム上の変異情報が集約されています。このようなゲノム配列情報をデータベースを通じて公開・共有することは、重複を回避した効率的な研究の実施と、さらなる医学的価値の高い成果の創出に必要不可欠であり、難病の原因変異やがんのドライバー変異の絞り込み、ゲノムワイド関連解析におけるジェノタイプ推定、薬の開発、副作用の軽減など、個の医療に資する有用な情報源となることが期待されます。
弊社への移管を機に、これまで多くのご要望を頂戴していたHGVDの商用利用もしていただけるようにいたしました。商用利用の際にお支払いいただく使用料で、継続的なHGVDのアップデートやメンテナンスにかかわる経費を賄い、これまで通り非営利の研究利用には無償でご利用いただきます。
The Human Genetic Variation Database (HGVD) is the first Japanese genetic variation database released in 2013. This database, which has been constructed and maintained by the Center for Genomic Medicine fo Kyoto University, and succeeded by GenoConcierge Kyoto, Inc., contains genomic variation information from approximately 4,200 samples covering the genetic background of Japanese population. The release and sharing of such genome sequence information through the database is essential for refined genetic analyses such as the efficient survey of causative mutations associated with intractable diseases or cancer, precise genotype imputation in genome-wide association studies, and prediction of side effects of drugs.
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Access to HGVD is subject to the Terms and Conditions of Use described on this page. Your use of HGVD constitutes your agreement to these Terms and Conditions of Use.
Acknowledgment for Publication
This work was supported by the Research Grant (201238002A) for Intractable Diseases from the Ministry of Health, Labor and Welfare of Japan.
HGVD Data Release
HGVD now provides genome variation data from two complementary datasets. The original release consists of exome sequencing data from 1,210 individuals. Five centers applied different combinations of exome capture kits and sequencing platforms on subsets of samples, and reads were aligned to the reference genome (NCBI Build 37) using the Burrows–Wheeler Aligner, or Novoalign for the YCU data. Downstream processing, including the removal of potential PCR duplicates, base-quality recalibration, local realignment, and variant calling, was performed with Samtools, Picard, and GATK. In this update we add whole genome sequencing data from 3,135 individuals representing the genetic diversity of the Japanese population, extending coverage beyond coding regions and enabling comprehensive variant discovery. Across this WGS cohort we identified 44,757,785 variants, of which 31.0% exhibiting a minor allele frequency of < 1% are novel, and the mean coverage is 20×.
Terms and Conditions of Use
Purpose of your use
HGVD Database published on 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 for educational or non-commercial research purpose use.
For those who desires to use this database for commercial use, please download HGVD Commercial License Agreement and send PDF copy of your signed Agreement to info@gckyoto.com in advance of your use.
Citation
Any use of data obtained from HGVD shall be cited in your publications. You may download or copy the content and other downloadable items displayed on the HGVD website, on the condition that you follow the citation format given below.
K. Higasa et al. "Human genetic variation database, a reference database of genetic variations in the Japanese population" J Hum Genet 61:547-553, 2016, doi: 10.1038/jhg.2016.12 link
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 link
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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. THIS SITE MAY INCLUDE LINKS TO OTHER WEBSITES OR DATABASES, HOWEVER, HGVD TAKES NO RESPONSIBILITY, WARRANTY OR GUARANTEE OVER THE NATURE OR CONTENT OF THOSE OTHER WEBSITES OR DATABASES. 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.
HGVD Commercial License Agreement
To use HGVD for commercial purposes, please fill out this Commercial License request form
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Download Human Genetic Variation Database
HGVD Data Version 3.00 Release — Whole-Genome Data from 3,135 Japanese Individuals Added
HGVD now provides genome variation data derived from two complementary datasets. The original release comprises exome sequencing data from 1,210 individuals. Five centers used different combinations of exome capture kits and sequencing platforms for subsets of samples, and the resulting reads were aligned to the reference genome (NCBI Build 37) using the Burrows–Wheeler Aligner, or Novoalign for the YCU data. Downstream processing—including the removal of potential PCR duplicates, base quality recalibration, local realignment, and variant calling—was performed using Samtools, Picard, and GATK.
In this update, we add whole-genome sequencing (WGS) data from 3,135 individuals representing the genetic diversity of the Japanese population, thereby extending coverage beyond coding regions and enabling comprehensive variant discovery. Across this WGS cohort, we identified 44,757,785 variants, 31.0% of which are novel, with a mean coverage of 20×.
HGVD データバージョン 3.00 公開 — 日本人 3,135 名の全ゲノムデータを追加
HGVD（Human Genetic Variation Database）は、2つの相補的なデータセットから構成されるゲノム変異データを提供しています。
初期リリースには、1,210 名の個人から得られたエクソームシーケンスデータが含まれています。5 つのセンターが、異なるエクソームキャプチャキットとシーケンシングプラットフォームの組み合わせを用いてサンプルのサブセットを解析し、リードは Burrows–Wheeler Aligner（YCU データについては Novoalign）を用いて参照ゲノム（NCBI Build 37）にアラインされました。その後の解析工程では、Samtools、Picard、GATK を用いて PCR 重複の除去、塩基品質の再較正、局所的なリアライメント、および変異検出が行われました。
今回のアップデート（バージョン 3.00）では、日本人集団の遺伝的多様性を網羅する 3,135 名の全ゲノムシーケンス（WGS）データ を新たに追加しました。これにより、遺伝子コーディング領域を超えた領域までカバレッジが拡張され、より包括的な変異の解釈が可能になっています。本 WGS コホート全体では 44,757,785 個の変異 が同定され、MAF1%未満の変異では 31.0％ が新規変異 でした。平均カバレッジは 20 倍（20×） です。
HGVD Release Version 3.00 (GRCh37/hg19) (10/21/2025)
HGVD Structural Variants Version 1.0 (GRCh37/hg19) (10/21/2025)
HGVD Release Version 2.30 (08/02/2017)
HGVD eQTL Release Version 8.1 (08/05/2015)
HGVD Japanese Reference Sequence Version 1.0 (GRCh37/hg19) (10/22/2015)
Contact
Educational or research purpose use
Center for Genomic Medicine, Graduate School of Medicine, Kyoto University
hgvd@genome.med.kyoto-u.ac.jp
South Research Bldg. No.1 (5F)
Kawahara-cho 53, Shogoin, Sakyo-ku, Kyoto-shi, Kyoto-hu, Japan
+81-75-751-4157
Commercial purpose use
GenoConcierge Kyoto, Inc.
Med-Pharm Collaboration Building
46-29 Yoshida-Shimo Adachi-cho, Sakyo-ku, Kyoto 606-8501 Japan
+81- 75-708-3545