dbSNP — NCBI Database of Single Nucleotide Polymorphisms

Overview

dbSNP is the NCBI open-access reference database for small-scale human genomic variants, established in 1998. It assigns stable Reference SNP identifiers (rs numbers) that serve as the canonical cross-database identifiers for variants across the genomics ecosystem. As of 2024 it holds over 1.1 billion unique RefSNPs from approximately 3,900 contributing labs in 81 countries. Since 2017 it covers human variants only, with non-human submissions redirected to the European Variation Archive (EVA).

Relationship to other NCBI variant databases

The NCBI variant database ecosystem divides submissions by data type and sensitivity. Variants with clinical significance assertions should be submitted to ClinVar, which accessions them and forwards the records to dbSNP for genome mapping and rs number assignment. Sensitive human genomic data that cannot be publicly released routes through dbGaP (controlled access). Large structural variants over 50 bp in length belong in dbVar, NCBI’s structural variation archive. dbSNP therefore holds the open-access, publicly released layer of human small variant data.

Connections

• Open-access counterpart: EVA (EMBL-EBI, Europe)
• Receives clinical variant accessions from: ClinVar
• Controlled-access complement: dbGaP

Resources

• https://www.ncbi.nlm.nih.gov/snp/ (dbSNP home)
• https://www.ncbi.nlm.nih.gov/snp/docs/submission/hts_launch_and_introductory_material/ (submission guide)
• https://doi.org/10.1093/nar/gkae1124 (Bhagwate et al. 2025, Nucleic Acids Research — 25-year overview)