Human Variation Databases

Abstract

Individual variations in genomic sequence are useful reagents in physical mapping, linkage analysis and the functional study of individual genes. Several public databases exist as comprehensive or specialized resources to organize these data for sequence annotation and research.

Keywords: single nucleotide polymorphism; microsatellite; genetic variation; haplotype, genome diversity

Web Links

ALFRED. A prototype project by the Kidd lab at Yale University to document allele frequencies in a broad, anthropological collection of human populations http://alfred.med.yale.edu/

dbSNP. The NCBI dbSNP database of genetic variation is currently the largest public database of sequence polymorphisms http://www.ncbi.nlm.nih.gov/SNP/

Ensembl. A software system which produces and maintains automatic annotation on eukaryotic genomes http://www.ensembl.org/

Ethnologue. A database of the world's languages. http://www.ethnologue.com/ http://www.ncbi.nlm.nih.gov/SNP/handle.html

Genome UCSC Browser. A data visualization tool provided by the University of California Santa Cruz to see features of genome sequence http://genome.ucsc.edu/cgi‐bin/hgGateway?org=human

HGVBase. A database developed to support genotype–phenotype association analyses http://hgvbase.cgb.ki.se/

The HGVBase site also maintains an annotated list of SNP‐related databases at http://hgvbase.cgb.ki.se/databases.htm

JSNP. The Japanese SNP database was developed as part of Japan's Millennium Project to identify up to 150000 sequence variations in gene regions over two years, to make the information related to these SNPs available to the public, and to develop analytical tools for polymorphisms http://snp.ims.u‐tokyo.ac.jp/

NCBI MapViewer. The Map Viewer supports search and display of genomic information by chromosomal position http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?

PubMed. A service of the National Library of Medicine, provides access to over 12 million MEDLINE citations back to the mid‐1960s and additional life science journals http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed

TSC. The SNP Consortium was formed as a nonprofit corporation in 1999 for providing public genomic data http://snp.cshl.org/

Online Mendelian Inheritance in Man. A textual catalog of human genes and genetic disorders. Web development and support is provided by The National Center for Biotechnology Information (NCBI) at the National Institutes of Health, Bethesda, MD, USA http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM

HGVS database index. The Human Genome Variation Society (HGVS) maintains an index of public variation and mutation databases http://www.genomic.unimelb.edu.au/mdi/dblist/dblist.html

MDI. As the forerunner to the HGVS, the HUGO Mutation Database Initiative (MDI) compiled a table of public mutation and variation databases http://ariel.its.unimelb.edu.au/∼cotton/glsdbg.htm

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How to Cite close
Sherry, Stephen T(Sep 2005) Human Variation Databases. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0005249]