Detection of regulatory SNPs in human genome using ChIP-seq ENCODE data.

ABSTRACT: A vast amount of SNPs derived from genome-wide association studies are represented by non-coding ones, therefore exacerbating the need for effective identification of regulatory SNPs (rSNPs) among them. However, this task remains challenging since the regulatory part of the human genome is annotated much poorly as opposed to coding regions. Here we describe an approach aggregating the whole set of ENCODE ChIP-seq data in order to search for rSNPs, and provide the experimental evidence of its efficiency. Its algorithm is based on the assumption that the enrichment of a genomic region with transcription factor binding loci (ChIP-seq peaks) indicates its regulatory function, and thereby SNPs located in this region are more likely to influence transcription regulation. To ensure that the appro

SUBMITTER: Bryzgalov LO 

PROVIDER: S-EPMC3812152 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature