ePIANNO

ePIANNO annotates ChIP-seq-derived genomic regions by integrating ChIP-seq and other NGS datasets with SNPs from the 1000 Genomes Project and NHGRI-curated GWAS data to enable analysis of transcription factor binding, histone modifications, chromatin accessibility, allele frequencies, and disease associations.

Key Features:

• Integration of diverse data sources: Combines ChIP-seq datasets (including hmChIP, ENCODE, and ROADMAP) with single nucleotide polymorphism (SNP) data from the 1000 Genomes Project and GWAS associations curated by NHGRI.
• Support for NGS-derived annotations: Processes and annotates genomic regions derived from next-generation sequencing (NGS) with focus on transcription factor binding sites, histone modifications, and chromatin accessibility.
• Comprehensive variant annotation: Reports genomic variations at transcription factor binding sites and histone-marked regions together with allele frequencies across populations.
• Cross-referencing with GWAS: Links regulatory elements to NHGRI GWAS findings to associate regulatory variation with disease-associated loci.
• Genomic-coordinate-based queries: Maps user-provided genomic coordinates or predefined regulatory regions to integrated SNP and GWAS annotations for locus-level interpretation.

Scientific Applications:

• Regulatory genomics: Investigating regulatory mechanisms of gene expression by combining ChIP-seq profiles with population genetic variation.
• Variant impact analysis: Assessing how SNPs affect transcription factor binding, histone modifications, and chromatin accessibility.
• Disease association interpretation: Prioritizing regulatory variants at GWAS loci to explore potential molecular links to disease etiology and progression.

Methodology:

Implements a web server architecture that accepts genomic coordinates or predefined regions, queries integrated ChIP-seq, 1000 Genomes SNP, and NHGRI GWAS datasets, and cross-references these sources to produce combined annotations.