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 rsid, SPDI, HGVS, or their genomic position. Many variant-associated edges are tagged with a
files_fileset accession linking to source files on the IGVF or ENCODE portals. See Data Sources and Field lineage for file format specifications and column-to-API field mappings.
Coding Variant Effects
Coding Variant Measurements (table)
This table presents measurements of effects of coding variants in experimental assays. Currently, this table presents IGVF data from 2 assays. VAMP-seq measures the effects of coding variants on protein abundance. Scores represent the weighted average of the variant across fluorescence bins. Scores are normalized to the median of the synonymous amino acid sequences at 1 and the median of the nonsense variants at 0. Lower scores indicate reduced abundance of the variant protein versus the wild type protein. SGE (saturation genome editing) measures the effects of single nucleotide variants and 3-base pair deletions on cell fitness. Scores are the estimated log2 fold change in relative variant abundance per day. Scores are normalized to the median synonymous score at 0. Lower scores represent reduced cell fitness for the specified variant in comparison to synonymous variants.Coding Variant Predictions (table)
This table presents predictions of general coding variants effects (pathogenicity, deleteriousness). Currently, this table presents IGVF predictions by 2 methods. MutPred2 predicts pathogenicity/deleteriousness of coding variants. Scores closer to 1 indicate higher deleteriousness/pathogenicity. ESM-1v predicts deleteriousness of coding variants. More negative scores indicate higher deleteriousness.Gene Regulation
Biosample Evidence (table)
This table shows experimental evidence per biosample for this variant.Enhancer-Gene Model Predictions (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). Only element-gene pairs with scores above the default model threshold are shown. Currently, this table includes predictions from the ENCODE-rE2G model across 1700 ENCODE biosamples (see Gschwind et al. bioRxiv 2023).
The table is initially sorted by Score in descending order, showing the strongest predictions first.
Allelic effect(s) on transcription factor binding (table)
This table shows effects of the variant on allelic binding in transcription factor (TF) ChIP-seq experiments.Molecular Networks
Coming soon!QTLs
Molecular QTLs (table)
This table shows quantitative trait loci (QTL) associated with this variant. Currently, these data include expression QTLs (eQTLs), splice QTLs (sQTLs) and chromatin accessibility QTLs (caQTLs) derived from the eQTL Catalogue and the African Functional Genomics Resource.Phenotypes
GWAS Association (table)
This table shows phenotypes (traits or diseases) associated with the variant through genome-wide association studies (GWAS).Population Data
Variants in Linkage Disequilibrium (table)
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.
Associated Disease (table)
This table shows diseases associated with this variant from ClinGen.Summary of data variant edges in the Knowledge Graph
Other Visualizations
The variant page includes several interactive visualization components that provide rich insights into variant effects, population genetics, and functional predictions.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
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
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
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
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