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About Ensembl Variation

The Ensembl Variation database stores areas of the genome that differ between individual genomes ("variants") and, where available, associated disease and phenotype information.

There are different types of variants for several species:

  • single nucleotide polymorphisms (SNPs)
  • short nucleotide insertions and/or deletions
  • longer variants classified as structural variants (including CNVs)

Explore the links below to learn more about Ensembl Variation:


For several different species in Ensembl, we import variant data (SNPs, CNVs, allele frequencies, genotypes, etc) from a variety of sources (e.g. dbSNP). Imported variants and alleles are subjected to a quality control process to flag suspect data.

We classify the variants into different classes and calculate the predicted consequence(s) of the variant and we have also created variant sets to help people retrieve a specific group of variants from a particular dataset.

In human, we calculate the linkage disequilibrium for each variant, by population.

See some examples of imported data on the Ensembl website (Human):

Location of a variant in the genome
Population genotypes and frequencies of a variant
Sample genotypes of a variant
Phenotype(s) associated with a variant


  • Daniel R Zerbino, Premanand Achuthan, Wasiu Akanni, M Ridwan Amode, Daniel Barrell, Jyothish Bhai, Konstantinos Billis, Carla Cummins, Astrid Gall, Carlos García Girón, Laurent Gil, Leo Gordon, Leanne Haggerty, Erin Haskell, Thibaut Hourlier, Osagie G Izuogu, Sophie H Janacek, Thomas Juettemann, Jimmy Kiang To, Matthew R Laird, Ilias Lavidas, Zhicheng Liu, Jane E Loveland, Thomas Maurel, William McLaren, Benjamin Moore, Jonathan Mudge, Daniel N Murphy, Victoria Newman, Michael Nuhn, Denye Ogeh, Chuang Kee Ong, Anne Parker, Mateus Patricio, Harpreet Singh Riat, Helen Schuilenburg, Dan Sheppard, Helen Sparrow, Kieron Taylor, Anja Thormann, Alessandro Vullo, Brandon Walts, Amonida Zadissa, Adam Frankish, Sarah E Hunt, Myrto Kostadima, Nicholas Langridge, Fergal J Martin, Matthieu Muffato, Emily Perry, Magali Ruffier, Dan M Staines, Stephen J Trevanion, Bronwen L Aken, Fiona Cunningham, Andrew Yates, and Paul Flicek
    Ensembl 2018
    Nucleic Acids Research
  • McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GRS, Thormann A, Flicek P and Cunningham F.
    The Ensembl Variant Effect Predictor
    Genome Biology 17:122(2016)

  • Rios D, McLaren WM, Chen Y, Birney E, Stabenau A, Flicek P, Cunningham F.
    A Database and API for variation, dense genotyping and resequencing data
    BMC Bioinformatics 11:238 (2010)

  • Chen Y, Cunningham F, Rios D, McLaren WM, Smith J, Pritchard B, Spudich GM, Brent S, Kulesha E, Marin-Garcia P, Smedley D, Birney E, Flicek P.
    Ensembl Variation Resources
    BMC Genomics 11(1):293 (2010)