Table 5.
Publicly available single-nucleotide polymorphism (SNP) databases.
| Name | Hosted by | URL | Features | Availability | Reference |
|---|---|---|---|---|---|
| UCSC | University of California, Santa Cruz, CA, USA | http://genome.ucsc.edu/ | Integrated browser displaying tracks built from annotation sets including SNPs, mRNA, disease association studies, and more | Web applet | Kent (68) |
| dbSNP | National Center for Biotechnology Information | http://ncbi.nlm.nih.gov/SNP/ | Central database of SNPs with integrated data from multiple population studies including the 1000 genome project | Web applet | Sherry et al. (48) |
| GWAS central (formerly HGVbase database) | Institutes, Consortia, and individual laboratories | http://gwascentral.org/ | Database of human genetic variation. Displays information on phenoytpes, genes, regions, or markers based on SNPs | Web applet | Fredman et al. (69) |
| ENSEMBL | European Bioinformatics Institute (EBI) | http://ensembl.org/ | Contains available genomes of multiple species. Displays summary information regarding isoforms, SNPs, and other features of genes or proteins | Web applet | Flicek et al. (70) |
| HapMap | National Center for Biotechnology Information | http://hapmap.ncbi.nlm.nih.gov/ | Contains integrated data of SNPs for haplotype analysis, finding tag SNPs, and for identifying GWAS hits | Web applet | Gibbs et al. (71) |
| 1000 Genome Project | European Bioinformatics Institute | http://1000genomes.org | Contains 1092 available human genomes for analysis as well as summary documentation regarding SNPs and other variation | FTP download | Abecasis et al. (72) |
| HaploView | The Broad Institute | http://broadinstitute.org/ | Calculates r2 and D′values for performing haplotype analysis of SNPs with HapMap data or user input data | For download on all major platforms | Barrett et al. (73) |
This list includes only SNP databases that focus on human and/or mouse sequences; other, more specialized databases may exist for other organisms. All databases listed accept novel SNPs from private and public organizations.