Cool things the Ensembl VEP can do: regulatory feature annotation

Most of the time when we talk about variant annotation, we talk about the effects of variants on genes, but did you know that the VEP can also tell you how variants affect the genomic features that regulate gene expression, such as promoter and enhancers?

CNX OpenStax [CC BY 4.0 (], via Wikimedia Commons

Regulatory features are annotated on the human and mouse genomes using publicly available ChIP-seq and similar data types to predict the locations of features that affect genes. Their activity is predicted in different cell types and tissues. Both the VEP script and online tool allow you to see the effects of variants in regulatory features, using the relevant drop-down or –regulatory tag respectively. The stable ID of the regulatory feature will appear in the Feature column of the output with the Feature Type column indicating that the feature is a Regulatory Feature and the Biotype column telling you if it’s a Promoter, Enhancer, CTCF-binding site etc.

You can also select a cell type of interest, which will filter the regulatory features to only show you those active in a tissue of interest. This is valuable if you’re investigating a phenotype that is restricted to a particular tissue.

The regulatory features are not linked to particular genes, however you can find the gene most likely to be affected by using the nearest gene option with the VEP script.