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NAR Molecular Biology Database Collection entry number 517
Kuroda M.1, Uchida N.1, Kawaguchi T.1, Yasuda E.1, Tanaka T.2, Takagi T.2 and Nakamura Y.2
1Bioinformatics Division, Japan Science and Technology Agency (BIRD, JST) , Tokyo, Japan.
2 Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan

Database Description

JSNP is a database of common gene variations in the Japanese population, located in genes or in adjacent regions that might influence the coding sequence of the genes. JSNP provides almost 195,000 SNPs and 84,500 allele frequencies. Integrated Maps which display mapping data from JSNP and public resources have been available to search and export data. Each variant has the latest genome annotation and experimental details. Downloads of JSNP are available in fasta and XML formats. Unrestricted access to JSNP and any associated files is available at

Recent Developments

A new data retrieval tool is available to narrow down JSNP or genes by keywords, SNP IDs, chromosomal position or variation features, and to select display items of the extracted data and download them in various formats. A new data set is available to search and show motifs which are predicted by InterPro and have non-synonymous amino acids substitution.


The project is one of Prime Minister's Millennium Projects.

It has been carried out by a collaboration of Human Genome Center (HGC), Institute of Medical Science (IMS), University of Tokyo and the Japan Science and Technology Agency (JST).

We thank Ministry of Education, Culture, Sports, Science and Technology in Japan for their support of SNP discovery and JSNP database development. We also wish to thank the Laboratory for Genotyping, the SNP Research Center, the Institute of Physical and Chemical Research (RIKEN) for the registry of SNPs in the genes encoding drug-metabolizing enzymes and drug transporters, and Japan Biological Informatics Consortium (JBIC) for the submission of allele frequency data.


1. Hirakawa M, Tanaka T, Hashimoto Y, Kuroda M, Takagi T, Nakamura Y. JSNP: a database of common gene variations in the Japanese population. Nucleic Acids Res. 2002, 30: 158-1562.

Go to the abstract in the NAR 2002 Database Issue.
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