disease-researchlisted

# Disease Research with ENCODE Functional Genomics ## When to Use - User wants to connect GWAS variants to ENCODE regulatory elements for disease mechanism research - User asks about "disease", "pathology", "therapeutic targets", "GWAS interpretation", or "clinical variants" - User needs to annotate disease-associated loci with functional genomics data from ENCODE - User wants to identify drug targets from epigenomic evidence using Open Targets integration - Example queries: "find enhancers disrupted by diabetes GWAS hits", "identify drug targets from ChIP-seq data", "connect my disease variants to regulatory elements" Leverage ENCODE's 926,535 cCREs and multi-layer functional data to understand disease mechanisms, interpret disease-associated variants, identify therapeutic targets, and connect genomic findings to clinical applications. ## Scientific Rationale **The question**: "How can ENCODE functional genomics help me understand a disease's molecular mechanisms and identify actionable targets?" Over 90% of disease-associated variants from GWAS fall in non-coding regions (Maurano et al. 2012). They disrupt regulatory elements controlling gene expression, not protein sequences. ENCODE provides the most comprehensive catalog of these elements across hundreds of cell types and tissues. This skill connects (1) genetic association data, (2) ENCODE functional annotations, and (3) clinical/pharmacological databases for druggable targets. ## Literature Foundation | Referenc