Single Nucleotide Polymorphisms (SNPs): What They Are and Why They Matter
No two human genomes are identical. The vast majority of human genetic variation takes the form of single nucleotide polymorphisms — SNPs (pronounced "snips") — positions in the genome where a single DNA base differs between individuals or populations. While any two humans are more than 99.9% genetically identical, the roughly 0.1% that differs — represented in hundreds of millions of SNPs distributed across the genome — accounts for much of the variation in traits, disease susceptibility, and drug responses that make each person biologically unique.
What Makes a SNP a SNP
A SNP is defined as a single base-pair variation at a specific position in the genome that is present in at least 1% of the population. This frequency threshold distinguishes SNPs from rare mutations, which may be present in a much smaller fraction of individuals. SNPs can occur anywhere in the genome: within genes (potentially affecting protein structure or function), in regulatory regions (potentially affecting gene expression), or in non-functional regions (where they may have no direct biological effect). The dbSNP database, maintained by NCBI, catalogues hundreds of millions of human SNPs with their genomic positions, frequencies across populations, and any known clinical associations.
Genome-Wide Association Studies (GWAS)
SNPs are the primary tool of genome-wide association studies, which compare SNP frequencies between large groups of individuals with and without a particular trait or disease. By genotyping hundreds of thousands to millions of SNPs across thousands of participants, GWAS can identify genomic regions where SNP frequencies differ significantly between cases and controls — implicating those regions in the biology of the trait. GWAS have identified thousands of disease-associated variants for conditions including type 2 diabetes, coronary artery disease, schizophrenia, Alzheimer's disease, inflammatory bowel disease, and many others. The identified variants often have individually small effects on risk but collectively explain a meaningful proportion of disease heritability.
SNPs in Pharmacogenomics
Some of the most clinically actionable SNP discoveries are in pharmacogenomics — the study of how genetic variation affects drug responses. SNPs in genes encoding drug-metabolising enzymes, transporters, and target receptors can determine whether a patient responds to a medication, experiences toxicity, or needs a different dose. The CYP2C19 gene, for example, contains SNPs that determine how quickly the prodrug clopidogrel is activated — an important consideration for cardiovascular patients. The PharmGKB database catalogues pharmacogenomic relationships, and clinical pharmacogenomic testing is increasingly used to guide prescribing decisions.
Population Genomics and Human History
At the population level, patterns of SNP variation tell the story of human migration, adaptation, and evolutionary history. SNPs that vary systematically between geographical populations reflect the genetic consequences of ancestral population movements, bottlenecks, and local adaptations. Consumer ancestry testing companies use panels of ancestry-informative SNPs to estimate the geographical origins of customers' genetic ancestry. Population genomics research uses SNP data to reconstruct ancient migration routes, identify signals of positive selection, and understand how human populations have adapted to different environments over tens of thousands of years.
Access our SNP catalogues and genomic variation databases, or contact us for guidance on SNP research tools and resources.