Single Nucleotide Polymorphism (SNP)


A single nucleotide polymorphism (SNP) is an abundant form of genome sequence variation comprising single base pair alternatives represented at a population frequency of more than 1%. SNPs contribute greatly to the genetic basis of phenotypic variation in ways yet to be fully understood.

Keywords: genome; variation; polymorphism; allele; haplotype

Figure 1.

Observed levels of nucleotide diversity (π) in and around human genes. A simple two‐exon gene is represented in genomic DNA and processed (mRNA) forms, with various subdomains (including degeneracy classes of coding nucleotides) marked to illustrate the typically observed levels of sequence variation reported across a range of publications. There is, however, a disparity in sequence variability of well over 10‐fold between different genes and chromosomal regions. cDNA: ; UTR: ; CDS: coding sequence.



Brookes AJ (1999) The essence of SNPs. Gene 234: 177–186.

Eyre‐Walker A and Keightley PD (1999) High genomic deleterious mutation rates in hominids. Nature 397: 344–734.

Foley R (1998) The context of human genetic evolution. Genome Research 8: 339–347.

Gray IC, Campbell DA and Spurr NK (2000) Single nucleotide polymorphisms as tools in human genetics. Human Molecular Genetics 9: 2403–2408.

Kimura M (1983) The Neutral Theory of Molecular Evolution. Cambridge, UK: Cambridge University Press.

Kwok P‐Y and Gu Z (1999) Single nucleotide polymorphism libraries: why and how are we building them? Molecular Medicine Today 5: 538–543.

Landegren U, Nilsson M and Kwok P‐Y (1998) Reading bits of genetic information: methods for single‐nucleotide polymorphism analysis. Genome Research 8: 769–776.

Lehväslaiho H (2000) Human sequence variation and mutation databases. Briefings Bioinformatics 1: 161–166.

Nei M and Li W‐H (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences of the USA 76: 5269–5273.

Schachter F (1998) Causes, effects, and constraints in the genetics of human longevity. American Journal of Human Genetics 62: 1008–1014.

Further Reading

Altshuler D, Pollara VJ, Cowles CR et al. (2000) An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407: 513–516.

Gould Rothberg BE (2001) Mapping a role for SNPs in drug development. Nature Biotechnology 19: 209–211.

Jiang C and Zhao Z (2006) Mutational spectrum in the recent human genome inferred by single nucleotide polymorphisms. Genomics 88: 527–534.

Jorde LB (2000) Linkage disequilibrium and the search for complex disease genes. Genome Research 10: 1435–1444.

Kristensen VN, Kelefiotis D, Kristensen T and Børresen‐Dale A‐L (2001) High‐throughput methods for detection of genetic variation. Biotechniques 30: 318–332.

Kruglyak L (1999) Prospects for whole‐genome linkage disequilibrium mapping of common disease genes. Nature Genetics 22: 139–144.

Kruglyak L and Nickerson DA (2001) Variation is the spice of life. Nature Genetics 27: 234–236.

Kwok P‐Y and Gu Z (1999) Single nucleotide polymorphism libraries: why and how are we building them. Molecular Medicine Today 5: 538–543.

Lercher MJ and Hurst LD (2002) Human SNP variability and mutation rate are higher in regions of high recombination. Trends in Genetics 18: 337–340.

Przeworski M, Hudson RR and Rienzo AD (2000) Adjusting the focus on human variation. Trends in Genetics 16: 296–302.

Schork NJ, Fallin D and Lanchbury JS (2000) Single nucleotide polymorphisms and the future of genetic epidemiology. Clinical Genetics 58: 250–264.

Syvänen AC (2001) Accessing genetic variation: genotyping single nucleotide polymorphisms. Nature Reviews Genetics 2: 930–942.

Weiss KM and Terwilliger JD (2000) How many diseases does it take to map a gene with SNPs? Nature Genetics 26: 151–157.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Brookes, Anthony J(Dec 2007) Single Nucleotide Polymorphism (SNP). In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0005006.pub2]