Genomics · Database
dbSNP
A public repository of human single nucleotide variations and short genetic variants for biomedical research.
What dbSNP is
The Single Nucleotide Polymorphism Database (dbSNP) is an open-access archive for short genetic variations developed by the National Center for Biotechnology Information (NCBI) in collaboration with the National Human Genome Research Institute (NHGRI). Established in September 1998 to complement GenBank, the database originally covered multiple species but ceased accepting and presenting non-human variant data in 2017. As of build 153, it contains hundreds of millions of distinct human variants derived from billions of submissions.
Despite its name, dbSNP catalogs a broader collection of short genetic variations beyond single nucleotide polymorphisms. These include small-scale insertions and deletions (indels), short tandem repeats (microsatellites), multinucleotide polymorphisms, heterozygous sequences, and named variants. Records incorporate population allele frequencies, genomic and RefSeq mappings, molecular consequences, and clinical significance for both common variations and disease mutations.
The resource functions as a centralised reference for genetic variation, supporting researchers investigating physical mapping, population genetics, evolutionary relationships, pharmacogenomics, and genotype-phenotype associations.
How it is organised
Variant data are submitted by individual laboratories, large-scale sequencing centres, and research consortia. Each accepted submission receives a permanent submitted SNP ID number (ss#). Identical submissions mapping to the same genomic position are grouped into a reference SNP cluster and assigned a reference SNP ID number (rs#). Submissions include metadata such as molecular type, organism, contact details, and experimental method.
Data are periodically released through new builds, occurring roughly every three to four months or alongside new genome assemblies. During these builds, submitted and reference variants are re-mapped to updated reference coordinates (such as GRCh37 or GRCh38). If multiple reference SNP clusters map to the identical position, the records are merged into the lowest rs# identifier, while obsolete identifiers remain queryable. Mergers are restricted if variants belong to different classes or if a record represents a clinically significant variant cited in scientific literature.
Key facts
- Launch date
- September 1998
- Organism scope
- Homo sapiens only (non-human variant support ended in 2017)
- Variant types
- Single nucleotide variations, indels, microsatellites/STRs, and multinucleotide polymorphisms
- Identifier types
- Submitted SNP ID (ss#) and Reference SNP ID (rs#)
- Database size
- Over 675 million distinct variants from nearly 2 billion submissions (as of build 153)
- Access interfaces
- Web search, Entrez, eUtils API, Variation Services, and FTP download
What you can use it for
- Variant annotation and identification
- Resolving rs# or ss# identifiers to retrieve genomic coordinates, flanking sequences, gene locations, and predicted amino acid changes.
- Population allele frequency evaluation
- Assessing global and study-wide minor allele frequencies across population studies, including datasets such as the ALFA project.
- Clinical variant investigation
- Filtering variations by clinical significance, such as pathogenic or likely pathogenic status, to support disease association and pharmacogenomic studies.
Query it here
The research agent queries dbSNP directly — no account, no API key — and every answer links back to the record it came from. Ask in plain language and it writes the query.
Strengths and limits
Good at
- Provides stable, widely used reference identifiers (rs#) that link to extensive NCBI genomic and literature resources.
- Aggregates population frequency metrics from large-scale cohorts, including dbGaP and the ALFA project.
- Preserves searchability of obsolete rs# numbers that have been merged into earlier records.
Watch out for
- No longer accepts, hosts, or updates genetic variation data for non-human organisms.
- Historical analyses have identified notable false positive rates resulting from alignment errors and paralogous gene differences.
Questions
Can I search dbSNP without writing code?
Yes. The research agent queries dbSNP directly, with no account or API key, and cites the record behind every answer. Ask in plain language — for a gene, a protein, a compound or a study — and it builds the query for you.
Can I reuse data from dbSNP?
dbSNP publishes its own terms of use; read them on https://www.ncbi.nlm.nih.gov/snp/ before reusing its records.
What is the difference between an ss# and an rs# number?
An ss# (submitted SNP number) identifies an individual laboratory submission, whereas an rs# (reference SNP cluster number) groups one or more identical ss# submissions mapped to the same genomic location.
Can I query dbSNP for non-human genetic variants?
No. Support for non-human variant submissions and presentation ended in late 2017, and the resource is now exclusively focused on human variations.
How are records merged when redundant variants are identified?
When two reference SNP clusters are mapped to the exact same position, dbSNP merges them under the lowest rs# ID. The larger ID is retired but remains searchable, unless the variant is clinically significant and cited in publications.
What validation evidence does dbSNP report for variants?
Validation categories include independent submissions, submitter confirmations, frequency or genotype data, presence in 1000 Genomes Project or HapMap data, and observation of all alleles across at least two chromosomes.
How to cite it
Sherry, S.T., Ward, M.H., Kholodov, M., Baker, J., Phan, L., Smigielski, E.M., Sirotkin, K. (2001). dbSNP: the NCBI database of genetic variation. Nucleic Acids Research, 29: 308–311.
Written from dbSNP's own website and reference material. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.