Skip to Main Content


How to use BioMart, Ensembl's data retrieval site

Recommended: Create an account at Ensembl

It's recommended that you create an account at Ensembl. This allows you to save searches, upload custom data tracks to the Genome Browser, save VEP (Variant Effect Predictor) results, and much more. Registration is free. Click the "Login/Register" link in the upper right corner of any Ensembl or BioMart page to register or login to an existing account.

Starting a Search in BioMart

When you enter the BioMart search page, the "New" button is highlighted (toward the upper left). As you search, you can always abandon your current query and start a search by clicking on the "New" button to start over.

To start, you select a database from the "CHOOSE DATABASE" drop-down menu.

  • Ensembl Genes: Retrieve genes and genomic annotation features from the genome of any of over 200 genomes available in the Ensembl Genome Browser. This is the dataset with the most features for most genomes, and it's a good place to start a search.
  • Mouse strains: Retrieve genes and annotation features from any of 15 different mouse strains.
  • Ensembl Variation: Retrieve short (SNP and Indel) variants or somatic (human only) or structural variants (not available for all species) from a number of species in Ensembl Genomes. This is a more complete set of variant annotations (especially for human) than what is available in the Ensembl Genes dataset.
  • Ensembl Regulation: Retrieve regulatory feature elements from human or mouse genomes. This is a more complete regulatory set than is available in Ensembl Genes.