LocusZoom

LocusZoom visualizes genetic association results and integrates gene models, linkage disequilibrium, GWAS and PheWAS signals, genomic annotations, chromatin co-accessibility, and eQTL measurements to support interpretation of loci and candidate causal variants.

Key Features:

• Locus plotting: Visualizes one or more traits in a genomic context showing gene models and genomic annotations.
• Linkage disequilibrium and reference panels: Enables selection of linkage disequilibrium (LD) reference panels for locus-specific LD annotation and comparisons.
• Causal variant identification: Supports identification of sets of likely causal variants through model refinement and comparative analyses.
• Extensible plot layouts and data layers: Provides pre-defined plot and panel layouts and data layers that can incorporate PheWAS results, chromatin co-accessibility, and eQTL measurements.
• Dataset harmonization and annotation: Harmonizes uploaded datasets by adding annotations to facilitate comparison and integration with external GWAS catalogs.

Scientific Applications:

• GWAS locus interpretation: Aids visualization and interpretation of genome-wide association study (GWAS) results to prioritize candidate causal variants.
• Cross-phenotype and functional integration: Integrates PheWAS, chromatin co-accessibility, and eQTL data with GWAS signals to assess functional effects and pleiotropy.

Methodology:

Interactive refinement of analysis models through user-driven selection and comparison of LD reference panels and GWAS catalogs, together with dataset harmonization by annotation.