A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast, the substitution of a purine with a pyrimidine (A or G/C or T) or vice versa is called a transversion. In SNPs, transitions are more prominent than transversions.

Different methods are used to study the genetic variations present in the genome, also known as genotyping. Unlike SNPs, single tandem repeats (STRs) involve di-, tri-, or tetranucleotide repeats. Scientists often use SNPs genotyping over STRs as SNPs are more abundant and stable, and some SNPs directly affect the phenotype.

Most of the time, SNPs are found in introns, which do not code for any protein. Such SNPs can be used as biological markers to locate genes associated with a particular disease. If the SNP is present within a gene or in a regulatory sequence near the gene, it may affect its function and cause disease.