SNPnexus

SNPnexus annotates and assesses the functional significance of single nucleotide polymorphisms (SNPs) and other genomic variations to prioritize known and novel variants for disease research and large-scale genotyping projects.

Key Features:

• Broad Annotation Scope: Covers SNPs, insertions/deletions, block substitutions, and variations represented using IUPAC codes.
• Functional Impact Assessment: Integrates seven major annotation systems to provide transcriptome- and proteome-level annotations and assess potential deleterious effects.
• Mapping and Cytogenetic Inference: Infers physical and cytogenetic mapping of variants.
• Regulatory and Structural Insights: Identifies overlaps with regulatory elements, structural variations, and conserved genomic regions.
• Integration with Genetic Databases: Provides HapMap genotype/allele data and links to previously reported genetic disease studies.
• Region-Based Analysis: Supports region-based analyses for targeted studies of specific genomic areas.
• Variant Prioritization: Evaluates and prioritizes known and novel SNPs within major biological models.

Scientific Applications:

• Disease Research: Identifies phenotypically important variants and helps prioritize genetic contributors to disease.
• Genomic Studies: Supports large-scale genotyping projects by supplying comprehensive variant annotations.
• Functional Genomics: Enables exploration of functional consequences of variants at transcriptome and proteome levels, including gene regulation and protein function.

Methodology:

SNPnexus uses an integrated approach combining data from seven major annotation systems and other databases to evaluate potential deleterious effects, infer physical and cytogenetic mapping, and identify overlaps with regulatory elements, structural variations, conserved genomic regions, and HapMap genotype/allele data linked to reported genetic disease studies.