Cracking the regulatory genome: Which genetic variants in DNase I sensitive regions are functional?
We developed a novel approach to annotating functional regulatory regions that integrates sequence information (e.g., position weight matrices) with DNaseI footprinting data to predict the impact of a sequence change on TF binding. We identified over 3 million regulatory variants predicted to affect active regulatory regions for a panel of TFs in over 650 cell-types.
Moyerbrailean GA, Kalita CA, Harvey CT, Wen X, Luca F, Pique-Regi R. (2016) Which Genetics Variants in DNase-Seq Footprints Are More Likely to Alter Binding? PLoS Genet 12(2): e1005875. doi: 10.1371/journal.pgen.1005875
We have provided annotations as a brower hub to facilitate viewing of the data. There are two tracks: 1) regulatory variants, and 2) regulatory footprints.
Launch UCSC browser with hub (new window)
The footprint annotation data is also available as bed files, separated both by cell-type and TF motif. Each file is formatted as bed9+ files, with four additional data fields: SNP position, 1KG reference allele, 1KG alternate allele, prior log ratio for binding of the reference allele, and the prior LR for binding of the alternate allele. For TFBS without a polymorphism, the SNP position is listed as "0" and the prior LR for the reference allele is repeated.
The supplemental excel files associated with the above publications can be downloaded here:
For questions related to the hub or the data, please contact: