# Single-nucleotide polymorphism (SNP)

A single-nucleotide polymorphism (SNP, said 'snip') is a germline variation at a single base-pair position. It exists where two or more nucleotide alleles occur in the population at a frequency above 1%. The human genome holds roughly 4 to 5 million common SNPs, about one per 500 to 1,000 base pairs of your DNA. They are genotyped with microarray chips that query hundreds of thousands of positions. SNPs are the main markers in genome-wide association studies (GWAS). A GWAS tests hundreds of thousands of variants against a trait or disease, across tens or hundreds of thousands of people. It is a statistical scan, not proof of cause. Because nearby SNPs are inherited together in blocks (high linkage disequilibrium, or LD), one 'tag' SNP can stand in for a whole haplotype. That cuts genotyping cost without losing discovery power, as the Phase II HapMap showed (Frazer et al., 2007). In aging genetics, many common SNPs each have a tiny effect. Added together into a polygenic risk score, they explain a meaningful slice of lifespan variation. Yashin et al. (2012) found 27 SNPs with consistent additive effects on lifespan across independent cohorts, pointing to pathways like cell growth and apoptosis. SNPs differ from rare variants (minor allele frequency below 1%). GWAS arrays mostly miss those, and whole-genome or whole-exome sequencing captures them better. Whether rare variants explain the heritability that common SNPs miss (the 'missing heritability') is still an open question.

## Sources

- International HapMap Consortium, Frazer KA, et al.. (2007). A second generation human haplotype map of over 3.1 million SNPs. Nature. https://doi.org/10.1038/nature06258
- Yashin AI, Wu D, Arbeev KG, Ukraintseva SV. (2012). Polygenic Effects of Common Single-Nucleotide Polymorphisms on Life Span: When Association Meets Causality. Rejuvenation Research. https://doi.org/10.1089/rej.2011.1257
- Buniello A, MacArthur JAL, Cerezo M, et al.. (2019). The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Research. https://doi.org/10.1093/nar/gky1120

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_Canonical: https://longevity-switzerland.com/en/glossary/snp · Part of Longevity Cities · Updated 2026-06-22_