RSAT Var-tools

RSAT Var-tools predicts and analyzes the impact of regulatory variants on transcription factor (TF) binding to assess how SNPs in regulatory regions alter gene regulatory activity.

Key Features:

• Prediction of Regulatory Variants: Predicts regulatory variants that may influence TF binding and helps identify candidate causal SNPs from GWAS.
• Variation Information Retrieval and Management: Facilitates acquisition and management of variant collections and interconversion between variation file formats.
• Sequence Retrieval Around Variants: Retrieves sequences surrounding variants to provide genomic context for allele-specific analyses.
• Motif Scanning Approaches: Performs motif scanning to compute changes in predicted TF binding affinity scores between alleles.
• Haplotype Analysis Support: Supports haplotype-level analysis to assess combined effects of linked variants on TF binding.

Scientific Applications:

• GWAS Variant Prioritization: Prioritizes noncoding SNPs from GWAS by predicting their effects on TF binding.
• Mechanistic Interpretation of Noncoding Variants: Provides allele-specific TF binding predictions to infer molecular mechanisms underlying gene regulation changes associated with phenotypes and diseases.
• Haplotype-level Regulatory Analysis: Enables analysis of combined variant effects on TF binding across haplotypes for studies of complex traits.
• Support for Basic and Applied Genomics: Facilitates interpretation of regulatory variation for both fundamental research and applied genomics investigations.

Methodology:

Computational steps explicitly include input of variant collections, interconversion between variation file formats, retrieval of sequences around variants, motif scanning to calculate allele-specific changes in TF binding affinity scores, and optional haplotype-level analysis.