SNP

A single nucleotide polymorphism (SNP) is a DNA sequence variation at a single nucleotide that is common in a population. In humans, a SNP is typically defined as a variation present in at least about 1% of individuals. SNPs occur throughout the genome and can be located in coding regions, noncoding regions, regulatory elements, or intergenic spaces.

Most SNPs have no direct effect on health or appearance, but some influence gene function, expression, splicing, or protein structure. In coding regions, SNPs can be synonymous (no amino acid change), missense (amino acid change), or nonsense (creates a stop codon). Regulatory or intronic SNPs can alter transcription factor binding, RNA processing, or chromatin state, potentially affecting phenotype.

SNPs are usually identified and catalogued with reference IDs (rs numbers) in databases such as dbSNP. Researchers assay SNPs using genotyping arrays that cover hundreds of thousands to millions of variants, or by DNA sequencing that captures known and novel SNPs. Minor allele frequency (MAF) describes how common the less frequent variant is in a population.

Applications of SNP data include genome-wide association studies (GWAS) to locate loci associated with diseases or traits, pharmacogenomics to predict drug response, and ancestry or population structure analyses. Many findings reflect linkage disequilibrium, where nearby SNPs are correlated, so a SNP may be a marker rather than the causal variant.

Limitations include that most SNPs have small effects and that associations can be population-specific. Interpreting SNPs requires integrating functional data and considering LD, calibration, and confounding factors.