LDassoc

LDassoc provides interactive visualization and integrates linkage disequilibrium, regulatory annotation, and candidate gene information to aid interpretation and prioritization of genome-wide association study (GWAS) results.

Key Features:

• Interactive Visualization: Produces dynamic plots and sortable tables for detailed examination of GWAS signals.
• Data Integration: Integrates linkage disequilibrium (LD) patterns, variant regulatory potential, and potential target genes.
• Population-Specific Analysis: Incorporates population-specific LD patterns to refine association signals across diverse populations.
• External Database Links: Links variants to external resources including the UCSC Genome Browser, dbSNP, and RegulomeDB.
• Variant Prioritization: Combines multiple data sources to prioritize variants for downstream functional studies.

Scientific Applications:

• Association Interpretation: Identification of significant genetic associations and assessment of their potential biological functions.
• Population Genetics: Enhanced analysis of population-specific genetic variation through population-specific LD evaluation.
• Functional Prioritization: Prioritization of candidate variants for follow-up functional assays and experimental validation.

Methodology:

Integrates LD patterns (including population-specific LD), variant regulatory annotations, and candidate target gene data, generates interactive plots and sortable tables, and links variants to UCSC Genome Browser, dbSNP, and RegulomeDB.