tooluniverse-regulatory-variant-analysis

This skill maps the causal chain from a genetic variant to its disease mechanism by querying regulatory context, target genes, molecular pathways, and phenotypic consequences across multiple evidence layers. It combines data from 7+ databases to construct evidence-graded mechanistic narratives for GWAS hits, eQTL variants, and non-coding regulatory elements.

Access histone ChIP-seq data, chromatin accessibility maps, and regulatory element annotations from ENCODE and Roadmap Epigenomics to investigate chromatin state by tissue, transcription factor binding patterns, and cis-regulatory landscapes. Interpret histone marks, eQTL associations, and variant regulatory impact through multi-layer evidence synthesis.

This skill maps transcription factor regulation by combining binding motif analysis, chromatin immunoprecipitation data, and expression quantitative trait loci to answer which TFs control a gene and which genes a TF targets. It separates direct regulatory evidence (ChIP-seq binding) from indirect signals (co-expression), integrates protein interaction networks, and grounds claims in perturbation experiments rather than computational prediction alone.

This skill systematically maps gene regulation by integrating transcription factor motifs (JASPAR), experimental ChIP-seq and chromatin data (ENCODE), regulatory variant scoring (RegulomeDB), and sequence-based deep-learning models to predict regulatory activity. Query what controls a gene, whether a variant hits a regulatory element, or how non-coding changes affect expression and accessibility.

Identify genes associated with diseases and traits by querying GWAS Catalog and Open Targets Genetics data. This skill ranks candidate genes using locus-to-gene scores that combine eQTL, chromatin interaction, and distance evidence—moving beyond simple nearest-gene approaches. Results include p-values, replication counts, and confidence levels to guide target prioritization for drug discovery and functional validation.

Access the GTEx portal's REST API to explore how genetic variants regulate gene expression across 54 human tissues. Find eQTL associations for your GWAS variants, retrieve tissue-specific expression levels, and identify splicing QTLs to uncover regulatory mechanisms underlying non-coding variants.