Monday, June 11, 2012

The HaploREG Database for Functional Annotation of SNPs

The ENCODE project continues to generate massive numbers of data points on how genes are regulated.  This data will be of incredible use for understanding the role of genetic variation, both for altering low-level cellular phenotypes (like gene expression or splicing), but also for complex disease phenotypes.  While it is all deposited into the UCSC browser, ENCODE data is not always the easiest to access or manipulate. 

To make epigenomic tracks from the ENCODE project more accessible for interpretation in the context of new or existing GWAS hits, Luke Ward and Manolis Kellis at the BROAD Institute have developed a database called HaploREG.  HaploREG uses LD and SNP information from the 1000 Genomes project to map known genetic variants onto ENCODE data, providing a potential mechanism for SNP influence.  HaploREG will annotate SNPs with evolutionary constraint measures, predicted chromatin states, and how SNPs alter the Positional Weight Matrices of known transcription factors.

Here's a screenshot from SNP associated with HDL cholesterol levels showing summary information for several SNPs in LD at R2>0.9 in CEU. Clicking each SNP link provides further info.

In addition to providing annotations of user-submitted SNPs, HaploREG also provides cross-references from the NHGRI GWAS Catalog, allowing users to explore the mechanisms behind disease associated SNPs.  Check out the site here: and explore the functionality of any SNPs you might find associated in your work.  The more functional information we can include in our manuscripts, the more likely they are to be tested in a model system.

HaploReg: Functional Annotation of SNPs

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Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License.