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Overview

The IGVF Catalog contains variant nodes primarily sourced from FAVOR.
Variants not present in FAVOR but present in the other variant collections below were also loaded.
Variants may be identified using SPDI, HGVS, or their genomic position.

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Choose the data type you need

• A row of cards now appears at the top of each variant page so you can jump straight to the evidence you want: Coding, Noncoding, Molecular Networks, Phenotypes, or Allele Frequencies.
• Pick a card to land on the matching section of the page and scan its tables without scrolling.
• The cards stay easy to tap on smaller screens, helping you quickly switch between coding changes, regulatory signals, network partners, phenotype associations, or population frequency summaries.

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Stay oriented across pages

• A colored coverage stripe now sits under the variant title, mirroring the home page bar so you instantly see how much IGVF evidence exists for each data type.
• Table headers now spell out whether rows come from datasets (for example, FAVOR or MaveDB experiments) or predictions (such as ENCODE E2G), making it clear when you are viewing measured results versus model outputs.
• SPDI and RefSeq-style variant identifiers now resolve cleanly even when they contain multiple colons—for example, NC_000023.11:154533039:G:C opens directly instead of showing an error.

Region links in the Gene Regulation section now open reliably for every chromosome label—chrX, chrY, chrM, and other reference contigs—so clicking a coordinate no longer leads to a blank page.

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Non-coding Variant Edges

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Variant Edges

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Enhancer-Gene Model Prediction Table

This table shows which genes are predicted to be regulated by enhancers overlapping the variant you’re viewing. Score ranges from 0 (no prediction) to 1 (confident prediction). Currently, this table includes predictions from the ENCODE-rE2G model across 1,458 ENCODE biosamples (see Gschwind et al. bioRxiv 2023) The table is initially sorted by Score in descending order, showing the strongest predictions first.

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Variants in Linkage Disequilibrium

This table lists variants in linkage disequilibrium with the query variant, and summarizes functional evidence about those variants. Each row reports one variant in one ancestry. LD information is sourced from 1000 Genomes Phase 3 queried from Ensembl. You can filter this table by ancestry using the dropdown menu above the table.

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GWAS Association

Which phenotypes are associated with this variant through genome-wide association studies? GWAS Catalog. Study IDs now open directly in the GWAS Catalog or UK Biobank (when applicable) so you can read the full study record without leaving the catalog page, and the previous Source column has been removed so the table stays focused on the study details shown here. CSV downloads now include the variant identifier in every exported row so your spreadsheets keep the context of the on-page tables.

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Coding variant measurements

Experimental assays now sit in their own table so you can focus on observed protein effects (for example, VAMP-seq abundance drops or SGE functional scores) without scrolling past prediction models. Hover the info bubbles in the Source column to see quick explanations of VAMP-seq or SGE when they appear, and use the updated VAMP-seq link to open variant plots directly at https://abundance.gs.washington.edu/plots/variants.

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Coding variant predictions

Computational models now have a separate table labelled Computational models, letting you review in silico scores (MutPred2, ESM-1v, AlphaMissense, REVEL, VEST4, BayesDel) without mixing them with wet-lab measurements. Legacy columns like SIFT, PolyPhen-2, CADD Raw, VARITY, and EVE have been removed to keep the view focused on current methods. Hover the question marks on MutPred2 Score and ESM-1v Score to see what each model measures.

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Allelic effect(s) on transcription factor binding

This table shows effects of the variant on allelic binding in transcription factor (TF) ChIP-seq experiments.

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Molecular Networks

A notice now appears at the top of this section reading “Perturb-seq and other CRISPR data coming soon!” so you know additional network evidence is on the way while you review the current results.

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Molecular QTLs

Molecular QTLs for the variant now appear in a single, streamlined table that combines gene-level and protein-level associations. Cell type and tissue names are shown with clear, human-readable labels. The table subtitle lists the contributing sources—GTEx, AFGR, EBI QTL Catalogue, and UK Biobank proteomics—so you can see provenance at a glance.

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Associated Disease

This table shows diseases associated with this variant from ClinGen and Orphanet.

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Functional assay measurement

This table shows functional assay measurements for each biosample, including AdAstra and GVATdb assay readouts for the variant.

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Interactive Visualizations

The variant page includes several interactive visualization components that provide rich insights into variant effects, population genetics, and functional predictions.

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Primary Variant Visualization

An animated visualization showing the molecular mechanism of the variant using SPDI notation. Features:

• Animated Sequence: Shows the variant change as deletion and insertion events
• Color Coding:
  • Teal (#337788): Insertion allele
  • Coral (#CC8877): Deletion allele
• Multi-phase Animation:
  • Initial display of deletion event
  • Fade-in of insertion allele
  • Arrow indicating the replacement direction
• Genomic Context: Displays surrounding genomic sequence with placeholder bases
• Responsive Design: Automatically adjusts to container width

This visualization helps users understand the molecular nature of the variant change at the nucleotide level.

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Allele Frequency Distribution

An interactive bar chart displaying population-specific allele frequencies from gnomAD. Features:

• Population Breakdown: Shows frequencies across major ancestry groups:
  • African, Amish, Ashkenazi Jewish, East Asian, Finnish
  • Native American, Non-Finnish European, Other, South Asian
• Interactive Elements:
  • Hover over bars to see exact frequency values
  • Color changes on hover for visual feedback
  • Precise tooltips with 3 significant figures
• Animated Rendering: Bars animate from bottom to top on initial load
• Rotated Labels: Population labels displayed at 45-degree angle for readability
• Responsive Scaling: Y-axis automatically scales to accommodate data range

This visualization provides crucial population genetics context for variant interpretation.

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Summary Data Table with Score Visualization

An interactive table combining functional prediction scores with visual progress bars. Features:

• Score Visualization: Each numerical score displayed with:
  • Horizontal progress bar showing relative magnitude
  • Color-coded bar (brand color) indicating score strength
  • Exact numerical value alongside visual representation
• Sortable Interface: Click column headers to sort by score values
• Dynamic Columns: Table adapts to show only relevant columns:
  • Functional class (when available)
  • Catalog links (when available)
  • Portal links (when available)
• Clamped Scoring: All scores normalized to 0-1 range for consistent visualization
• Loading States: Graceful handling of data loading with appropriate placeholders

This component allows quick visual comparison of functional prediction scores across different tools and databases.

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Linkage Disequilibrium Heatmap

An interactive heatmap showing pairwise linkage disequilibrium relationships with nearby variants. Features:

• Dual Metrics: Toggle between r² and D’ measurements using dropdown selector
• Interactive Exploration:
  • Hover over cells to see detailed LD statistics
  • Tooltips display both variant IDs and precise r²/D’ values
  • Mouse tracking with real-time feedback
• Color Gradient: Intensity represents LD strength (white to teal)
• Variant Organization: Variants automatically sorted by genomic position
• Export Functionality: Download heatmap as PNG image
• Responsive Design: Square aspect ratio that scales with container
• Legend: Color scale reference showing value mapping

The heatmap reveals local LD structure and helps identify variant clusters that may represent the same causal signal.

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Ancestry Filtering

An animated interface for filtering LD data by population ancestry. Features:

• Smooth Transitions: Framer Motion animations for state changes
• Toggle Interaction:
  • Click ancestry labels to filter data
  • Selected ancestry highlighted with brand color
  • Clear button (×) to remove filter
• Population Mapping: Displays both short codes and full population names:
  • ASJ (Ashkenazi Jewish), EAS (East Asian), AFR (African)
  • FIN (Finnish), NFE (Non-Finnish European), SAS (South Asian)
  • AMI (Amish), OTH (Other), AMR (American), EUR (European)
• Dynamic Visibility: Only shows when multiple ancestries are available
• Hover Effects: Scale animations on hover for visual feedback

This component enables population-specific analysis of linkage disequilibrium patterns.