SNPs

A single nucleotide polymorphism, or SNP, is a variation at a single position in the genome that is common in a population. By definition, a SNP must be present in at least about 1% of individuals. SNPs are the most frequent type of genetic variation among people and can occur in coding or non-coding regions of the genome.

SNPs can influence biology in several ways. Some occur in protein-coding regions and change an amino acid or introduce a stop codon; many are synonymous changes with no effect on the protein. Others lie in regulatory regions and can affect when, where, or how much a gene is expressed. However, the majority of SNPs do not have a discernible impact on phenotype.

Because SNPs are abundant and often inherited together in blocks, they are widely used as genetic markers. Genome-wide association studies rely on SNPs to identify regions of the genome associated with diseases, traits, or drug responses. A detected association may point to a nearby causal variant and can help map risk loci even when the exact functional variant is not known.

A well-known example is the SNP rs4988235, where the T allele is associated with lactase persistence in adults of many European ancestries. Another set of SNPs, rs429358 and rs7412, define APOE alleles linked to Alzheimer’s disease risk. These examples illustrate how SNPs can influence traits or serve as tools in research, rather than acting as direct causes in all cases.

Technologies such as SNP genotyping arrays and whole-genome sequencing are used to identify SNPs. Analyses focus on allele frequencies, genotype distributions, and statistical associations, with attention to population structure and multiple testing. Applications span disease risk prediction, pharmacogenomics, ancestry inference, and forensic genetics, while limitations include population-specific frequencies and the fact that many associations are correlative rather than causal.