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:


Examples

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
Citations

References

Ensembl

Fergal J Martin, M Ridwan Amode, Alisha Aneja, Olanrewaju Austine-Orimoloye, Andrey G Azov, If Barnes, Arne Becker, Ruth Bennett, Andrew Berry, Jyothish Bhai, Simarpreet Kaur Bhurji, Alexandra Bignell, Sanjay Boddu, Paulo R Branco Lins, Lucy Brooks, Shashank Budhanuru Ramaraju, Mehrnaz Charkhchi, Alexander Cockburn, Luca Da Rin Fiorretto, Claire Davidson, Kamalkumar Dodiya, Sarah Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos Garcia Giron, Thiago Genez, Gurpreet S Ghattaoraya, Jose Gonzalez Martinez, Cristi Guijarro, Matthew Hardy, Zoe Hollis, Thibaut Hourlier, Toby Hunt, Mike Kay, Vinay Kaykala, Tuan Le, Diana Lemos, Diego Marques-Coelho, José Carlos Marugán, Gabriela Alejandra Merino, Louisse Paola Mirabueno, Aleena Mushtaq, Syed Nakib Hossain, Denye N Ogeh, Manoj Pandian Sakthivel, Anne Parker, Malcolm Perry, Ivana Piližota, Irina Prosovetskaia, José G Pérez-Silva, Ahamed Imran Abdul Salam, Nuno Saraiva-Agostinho, Helen Schuilenburg, Dan Sheppard, Swati Sinha, Botond Sipos, William Stark, Emily Steed, Ranjit Sukumaran, Dulika Sumathipala, Marie-Marthe Suner, Likhitha Surapaneni, Kyösti Sutinen, Michal Szpak, Francesca Floriana Tricomi, David Urbina-Gómez, Andres Veidenberg, Thomas A Walsh, Brandon Walts, Elizabeth Wass, Natalie Willhoft, Jamie Allen, Jorge Alvarez-Jarreta, Marc Chakiachvili, Bethany Flint, Stefano Giorgetti, Leanne Haggerty, Garth R Ilsley, Jane E Loveland, Benjamin Moore, Jonathan M Mudge, John Tate, David Thybert, Stephen J Trevanion, Andrea Winterbottom, Adam Frankish, Sarah E Hunt, Magali Ruffier, Fiona Cunningham, Sarah Dyer, Robert D Finn, Kevin L Howe, Peter W Harrison, Andrew D Yates, Paul Flicek
Ensembl 2023
Nucleic Acids Res. 2023, vol. 51(D1):D933-D941
doi:10.1093/nar/gkac958

Ensembl Variation

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
doi:10.1093/database/bay119

Haplosaurus

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)
doi:10.1038/s41467-018-06542-1

VEP

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)
doi:10.1186/s13059-016-0974-4