Position dependent variant effects reveal importance of context in genomic regulation

This repository contains the analysis code and supporting materials for studying how the positional context of genetic variants influences regulatory activity. The project integrates experimental variant effect data, model-based predictions, clustering, and in silico mutagenesis to characterize context-dependent regulatory mechanisms.

Directory Structure

├── README.md
├── figures
└── src
    ├── 1-GTeX_experimental_variant_effect
    ├── 2-opentargets_model_variant_effect
    ├── 3-cluster_variant_effects
    ├── 4-range_variant_effect_TFs
    ├── 5-TF_position
    ├── 6-ism_variant_effects
    ├── 7-investigating_sines
    ├── 8-predict_alphagenome
    └── 9-schematic

Citation

If you use this code, please cite:

Position-dependent variant effects reveal the importance of context in genomic regulation. bioRxiv. https://doi.org/10.64898/2026.03.17.712488