Typical Epigenetic outputs

• Peak calling & annotation with biological context
• Motif discovery → transcription factor activity inference
• Regulatory network reconstruction with mechanistic hypotheses
• Enhancer-promoter linking using chromatin architecture
• Cell-type specific element identification
• Integration with genetic variants (QTL/GWAS colocalization)/transcriptomics
• Differential analysis adjusted for biological confounders
• Biomarker prioritization for clinical translation
• Validation strategy design (orthogonal assays)