๐งฌ MAGI Variant Interpreter
Variant interpretation demo built on the NTv3 foundation model
MAGI combines NTv3 sequence predictions with annotation, ranking, and rule-based summaries to help review variant-associated signals in a local genomic window.
The app reports changes across:
- Regulatory elements (promoters, enhancers, CTCF sites)
- Structural features (coding sequence, splice sites, UTRs)
- Epigenetic marks (histone modifications, chromatin accessibility)
- Context-dependent tracks (for example CAGE and chromatin assays)
Attribution: MAGI was developed by Dan Ofer, Stav Zok, and Michal Linial.
This web app extends MAGI with multi-species support: 15+ animals and 6 plants can be scored via Ensembl REST APIs for on-the-fly sequence fetching. Human remains the primary supported species with full BigWig and MANE transcript annotation.
๐ข Model ready โ Device: cpu โข Sequence source: local-2bit โข Tracks: 21 BED + 3602 BigWig
Manual Variant Input
Enter a single variant for detailed scoring and interpretation. Human defaults to GRCh38/hg38. For non-human species, coordinates should match the selected species assembly available through Ensembl.
Human: chr1โchr22, chrX, chrY, chrM. Non-human: bare names (e.g., 1, X, MT) or with chr prefix. Coordinates should match your species' current Ensembl assembly.
Results
Top ranked tracks (BED + BigWig, ordered by |ฮ|)
Reference (dashed gray) vs alternate signal for the top disrupted tracks. Red shading = gain of function, blue shading = loss of function. The slider maximum updates to the available track span for the current prediction.