CONQUER

CONQUER facilitates comprehensive interpretation of the functional consequences of GWAS hits, with emphasis on variants in non-coding and intergenic regions.

Key Features:

• Genome build alignment: Aggregates and aligns data to the GRCh38/hg38 reference build.
• Data integration: Integrates static and dynamic repositories including GTExPortal, the Epigenomics Project, the 4D genome database, and genome browsers.
• Non-coding/intergenic focus: Emphasizes interpretation of single nucleotide polymorphisms (SNPs) located in non-coding and intergenic regions.
• Multi‑SNP and network analysis: Analyzes multiple SNPs simultaneously and represents risk loci as interconnected network elements.
• Interactive visualization: Produces interactive visual data representations to explore underlying datasets and relationships among variants.
• Regulatory inference: Integrates epigenomic and expression data to support inference of regulatory mechanisms affecting gene expression.
• Tissue-specific expression linking: Links SNPs to gene expression patterns across tissues using GTExPortal data.

Scientific Applications:

• Interpretation of non-coding GWAS hits: Elucidates potential functional consequences of GWAS-identified variants outside coding regions.
• Tissue-specific expression analysis: Associates SNPs with tissue-specific gene expression profiles via GTExPortal.
• Epigenetic mechanism inference: Combines epigenomic datasets to infer regulatory mechanisms underlying variant effects.
• 3D genome interaction exploration: Uses 4D genome data to assess spatial genome organization relevant to variant function.
• Variant and locus prioritization: Aids prioritization of candidate causal variants and risk loci from GWAS results.
• Network-level genetic analysis: Supports evaluation of how multiple risk loci interact within broader regulatory networks.

Methodology:

Aggregates data from static and dynamic repositories aligned to GRCh38/hg38 (including GTExPortal, Epigenomics Project, 4D genome database, and genome browsers), performs simultaneous multi‑SNP analysis treating loci as interconnected network elements, and generates interactive visualizations for dataset exploration.