Ensembl Variation - Data access

Ensembl variation data can be accessed through:

• The website
• BioMart
• The FTP site
• The Perl API
• The REST API
• The MySQL database

Website

Variant data can be viewed in the browser through pages such as:

• Gene: Variation Table and Variation Image (for all variants in a gene) e.g. for all variants in KCNE2. Structural Variation to see all structural variants overlapping the gene.
• Transcript: Population comparison, Comparison image (for comparing variants in a transcript across different individual or strain sequences) e.g. compare Tmco4 in different mouse strains
• Transcript: Sequence, protein: list of the coding variants in protein coordinates.
• Location: Region in Detail (Variants can be drawn using "Configure this page" at the left. The menu allows display of information in Ensembl databases along with external sources in DAS format such as DGV loci.)
• Phenotype: A karyotype view to display the variants associated with a certain phenotype, e.g. phenotype "Glaucoma".

Examples:

Gene

Variation Table

Transcript

Variation Table

Transcript

Protein Variation

Location

Region in detail

Phenotype

Karyotype view

Clicking on any variant on an Ensembl page will open a Variation tab with information about the flanking sequence and source for the selected variant. Links to linkage disequilibrium (LD) plots, phenotype information (for human) from EGA, OMIM and NHGRI-EBI and Ensembl genes and transcripts that include the variant can be found at the left of this tab. You may also view multiple genome alignments of various species, highlighting the variant. Ancestral sequences are included in this display.

Here are some webpage examples of different types of variants:

• SNP - example of a SNP home page.
• InDel - example of a deletion home page.
• Structural variant (CNV) - example of a structural variant home page.
• Somatic variant - example of a somatic variant.

BioMart

BioMart can be used to export custom tables of variation data in Ensembl. Human has four variation databases in Ensembl:

• Short variants
• Somatic short variants
• Structural variants
• Somatic structural variants

All variant databases can be filtered by genes and consequences, genomic loci, phenotype and source, amongst others. BioMart is not a suitable method to export tables of all variants in a genome, and we recommend that you filter the data.

See the BioMart documentation.

FTP site

Whole genome VCF files can be found on the Ensembl FTP site. As well as files of just the variants by location, some species may have files which include phenotypes or individual genotypes.

Perl API

A comprehensive Perl Application Programme Interface (API) provides efficient access to the Ensembl Variation database.

• API Installation : A step-by-step installation guide for all Perl Ensembl APIs.
• Variation API Documentation : A complete reference to the objects and methods used in the Variation database API, through the Doxygen tool.
• Variation API Tutorial : An introduction to the underlying concepts of the Variation database API.

REST API

A language agnostic RESTful API allows flexible access to the Ensembl Variation database.

• User Guide : Sample clients and information for using the Ensembl REST APIs.
• REST Endpoints : A complete reference to the Endpoints used in the Ensembl REST API.

MySQL database

• Schema documentation : page describing every column of every table of the Ensembl Variation database schema.
• Database diagram [PDF]: