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A SNP (single nucleotide polymorphism, pronounced “snip”) is a position in the genome where people differ by a single DNA building block. In genetics research it is the most common type of variation between individuals, and it is the unit behind most genotyping arrays, association studies and variant databases. This guide covers the definition, how common SNPs really are, what researchers use them for, and how to look one up in dbSNP.
What a SNP is (and how it differs from a SNV or an indel)
The National Human Genome Research Institute (NHGRI) defines a SNP as a genomic variant at a single base position. MedlinePlus (NIH, National Library of Medicine) describes it as a difference in a single DNA building block, called a nucleotide. Scientists study whether and how SNPs in a genome influence health, disease, drug response and other traits.
Two points of usage matter when you write a methods section:
- The frequency convention. MedlinePlus counts a variant as a SNP when it is found in at least 1 percent of the population. NHGRI’s definition names no frequency threshold, so the two sources are not identical. State which definition you are applying.
- An rsID is not always a SNP. NCBI’s dbSNP catalogs SNPs, short insertions and deletions (indels), microsatellites and small structural variations. A reference SNP ID (rsID) therefore identifies a catalogued variant, not necessarily a single-base change.
How common SNPs are
Three different numbers circulate, and they count different things:
- Per person: MedlinePlus says SNPs occur almost once in every 1,000 nucleotides on average, which means roughly 4 to 5 million SNPs in a person’s genome.
- Across populations: MedlinePlus states that more than 600 million SNPs have been found in populations around the world.
- In dbSNP: the dbSNP About page reports 5.0 billion submitted SNPs (ss numbers) and 1.2 billion unique reference SNPs (rs numbers), checked 2026-10-29. These are database records, including non-SNP variant classes, not a count of distinct human polymorphisms.
Do not quote one of these figures as if it answered a different question: a per-genome count, a population catalogue and a database total are three separate denominators.
What SNPs are used for in research
MedlinePlus lists three main uses. SNPs act as biological markers that help scientists locate genes associated with disease. They can help predict an individual’s response to certain drugs. They can also be used to track the inheritance of disease-associated variants within families.
Most SNPs are found in the DNA between genes. A SNP inside a gene or in a regulatory region may affect gene function more directly. For the statistics of testing millions of SNPs at once, see genome-wide significance thresholds in GWAS.
Where to access SNP data
NCBI’s dbSNP, launched in 1998, is a freely accessible public database that catalogs small genetic variations. Its reference SNP IDs (rsIDs) allow consistent tracking of a variant across studies and databases. CASRAI’s dbSNP entry gives the short definition; the primary source is the dbSNP About page.
How to look up a SNP in dbSNP
- Open the dbSNP portal at https://www.ncbi.nlm.nih.gov/snp/.
- Search by whichever identifier you have. The portal supports searching for SNPs using rsIDs, gene names, genomic coordinates and functional classifications.
- To restrict a search to a gene, use an Entrez field tag, for example
BRCA1[GENE]. - Open the record for the rsID you need and note the date you checked it.
Reading an rsID
An rsID such as the ones dbSNP assigns is an identifier for a catalogued variant, not a description of its effect. Because dbSNP also holds indels and microsatellites, check the variant type on the record before calling something a SNP. When you report one, give the rsID, the date you checked it, and the genome assembly your coordinates refer to. If your variants arrive in a sequencing file, reading a VCF file explains how the identifiers and fields appear there.
Free resources
| Resource | What it provides |
|---|---|
| dbSNP (NCBI) | Free public catalog of small genetic variations, searchable by rsID, gene name, coordinates and functional class |
| MedlinePlus Genetics (NIH) | Plain-language explanation of SNPs, frequency and uses |
| NHGRI Genetics Glossary | Formal definition of a SNP at a single base position |
For population and clinical variant resources, see the CASRAI entries on the 1000 Genomes Project, gnomAD and ClinVar.
FAQ
Is SNP pronounced “snip”?
Yes. NHGRI gives the abbreviation SNP, pronounced “snip”.
How many SNPs are in the human genome?
A single person carries roughly 4 to 5 million SNPs, according to MedlinePlus, while more than 600 million SNPs have been identified across world populations. dbSNP’s larger totals count database records of several variant types.
Is every variant with an rsID a SNP?
No. dbSNP also catalogs short indels, microsatellites and small structural variations.
Sources
- MedlinePlus Genetics, “What are single nucleotide polymorphisms (SNPs)?” (NIH, National Library of Medicine): https://medlineplus.gov/genetics/understanding/genomicresearch/snp/ (checked 2026-10-29)
- NHGRI Genetics Glossary, “Single Nucleotide Polymorphisms”: https://www.genome.gov/genetics-glossary/Single-Nucleotide-Polymorphisms (checked 2026-10-29)
- NCBI dbSNP, About: https://www.ncbi.nlm.nih.gov/snp/docs/about/ (checked 2026-10-29)
