ensembl-annotationlisted

# Query the Ensembl REST API ## When to Use - User wants to annotate variants with Ensembl VEP (Variant Effect Predictor) consequences - User asks about "VEP", "Ensembl", "variant annotation", "regulatory build", or "gene annotation" - User needs to convert coordinates between assemblies using Ensembl's liftover API - User wants to check the Ensembl Regulatory Build for overlap with ENCODE elements - Example queries: "run VEP on my variant list", "annotate SNPs with regulatory consequences", "check Ensembl regulatory build for my peaks" Annotate variants, look up regulatory features, convert coordinates, and resolve gene identifiers using the Ensembl REST API. ## Scientific Rationale **The question**: "What does the Ensembl Regulatory Build say about this region, and what is the predicted effect of this variant?" The Ensembl Regulatory Build integrates ENCODE, Roadmap Epigenomics, and Blueprint data into a unified annotation of regulatory features across human cell types. The Variant Effect Predictor (VEP) is the standard tool for variant consequence prediction, integrating 50+ annotation sources including CADD, REVEL, SpliceAI, and AlphaMissense. ### Ensembl ↔ ENCODE Feedback Loop Ensembl's Regulatory Build incorporates ENCODE ChIP-seq, DNase-seq, and CTCF data to define regulatory features. Querying Ensembl after an ENCODE analysis provides an independent, aggregated view of regulatory annotations — often including data from non-ENCODE sources (Blueprint, Roadmap) t