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 human, including some with restricted access:

  • 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


  • Fiona Cunningham, Premanand Achuthan, Wasiu Akanni, James Allen, M Ridwan Amode, Irina M Armean, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, Carla Cummins, Claire Davidson, Kamalkumar Jayantilal Dodiya, Astrid Gall, Carlos García Girón, Laurent Gil, Tiago Grego, Leanne Haggerty, Erin Haskell, Thibaut Hourlier, Osagie G Izuogu, Sophie H Janacek, Thomas Juettemann, Mike Kay, Matthew R Laird, Ilias Lavidas, Zhicheng Liu, Jane E Loveland, José C Marugán, Thomas Maurel, Aoife C McMahon, Benjamin Moore, Joannella Morales, Jonathan M Mudge, Michael Nuhn, Denye Ogeh, Anne Parker, Andrew Parton, Mateus Patricio, Ahamed Imran Abdul Salam, Bianca M Schmitt, Helen Schuilenburg, Dan Sheppard, Helen Sparrow, Eloise Stapleton, Marek Szuba, Kieron Taylor, Glen Threadgold, Anja Thormann, Alessandro Vullo, Brandon Walts, Andrea Winterbottom, Amonida Zadissa, Marc Chakiachvili, Adam Frankish, Sarah E Hunt, Myrto Kostadima, Nick Langridge, Fergal J Martin, Matthieu Muffato, Emily Perry, Magali Ruffier, Daniel M Staines, Stephen J Trevanion, Bronwen L Aken, Andrew D Yates, Daniel R Zerbino, and Paul Flicek
    Ensembl 2019
    Nucleic Acids Research
  • Sarah E Hunt, William McLaren, Laurent Gil, Anja Thormann, Helen Schuilenburg, Dan Sheppard, Andrew Parton, Irina M Armean, Stephen J Trevanion, Paul Flicek, Fiona Cunningham
    Ensembl variation resources
    Database Volume 2018
  • William Spooner, William McLaren, Timothy Slidel, Donna K. Finch, Robin Butler, Jamie Campbell, Laura Eghobamien, David Rider, Christine Mione Kiefer, Matthew J. Robinson, Colin Hardman, Fiona Cunningham, Tristan Vaughan, Paul Flicek and Catherine Chaillan Huntington
    Haplosaurus computes protein haplotypes for use in precision drug design.
    Nature Communications 9:4128(2018)
  • 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)