Annotating and prioritizing human non-coding variants with RegulomeDB v.2
Abstract
N early 90% of the disease riskassociated variants identified by genome-wide association studies are in non-coding regions of the genome. The annotations obtained by analyzing functional genomics assays can provide additional information to pinpoint causal variants, which are often not the lead variants identified from association studies. However, the lack of available annotation tools limits the use of such data. To address the challenge, we previously built the ‘RegulomeDB database’ to prioritize and annotate variants in non-coding regions, which has been a highly utilized resource for the research community (Supplementary Fig. 1). Here we present an update of the RegulomeDB web server, RegulomeDB v.2 (http:// regulomedb.org). RegulomeDB annotates a variant by intersecting its position with genomic intervals identified from functional genomic assays and computational approaches. It also incorporates variant hits into a heuristic ranking score, representing its potential to be functional in regulatory elements. We improve and boost annotation power by incorporating thousands of newly processed data from functional genomic assays in GRCh38 assembly and include probabilistic scores from the SURF algorithm that was the top performing non-coding variant predictor in the Fifth Critical Assessment of Genome Interpretation (CAGI-5). The update of RegulomeDB now includes more than 650 million and 1.5 billion genomic intervals in hg19 and GRCh38, respectively — a fivefold increase…
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