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About Ensembl Variation | Data Description | Predicted Data | Database Description | Perl API | Variant Effect Predictor

About Ensembl Variation

The Ensembl database has structural variants and sequence variants (including Single Nucleotide Polymorphisms (SNPs), insertions, deletions and somatic mutations) for several species.
We predict the effects of variants on the Ensembl transcripts and regulatory features for each species. You can run the same analysis on your own data using the Variant Effect Predictor.
This data is integrated with the other data sources in Ensembl and available on the website and via the Perl API for programmatic access to the variation data.

The Ensembl Variation documentation is divided in 4 parts:


  • Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, Gordon L, Hendrix M, Hourlier T,
    Johnson N, Kähäri AK, Keefe D, Keenan S, Kinsella R, Komorowska M, Koscielny G, Kulesha E, Larsson P, Longden I, McLaren W, Muffato M, Overduin B, Pignatelli M,
    Pritchard B, Riat HS, Ritchie GR, Ruffier M, Schuster M, Sobral D, Tang YA, Taylor K, Trevanion S, Vandrovcova J, White S, Wilson M, Wilder SP, Aken BL, Birney E,
    Cunningham F, Dunham I, Durbin R, Fernåndez-Suarez XM, Harrow J, Herrero J, Hubbard TJ, Parker A, Proctor G, Spudich G, Vogel J, Yates A, Zadissa A, Searle SM.
    Ensembl 2012
    Nucleic Acids Research 40(D1):D84-D90(2012)

  • McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F.
    Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor.
    BMC Bioinformatics 26(16):2069-70(2010)

  • 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)