Identifying non-coding variant effects at scale via machine learning models of cis-regulatory reporter assays

Note (25 September 2026): Due to ongoing technical issues with Zenodo's upload service, the following files are not yet available in this version of the record: gnomAD (v3.1.2 SNPs and small indels) — Supplementary Dataset 8 Saturation mutagenesis of human promoters — Supplementary Dataset 9 Saturation mutagenesis of ENCODE dELSs — Supplementary Dataset 12 MPAC model artifacts — Supplementary Dataset 16 These files are unchanged from the previous version of this record, where they remain permanently available at 10.5281/zenodo.20694870. They are also mirrored at https://huggingface.co/datasets/saarantras1/mpac-predictions. We will add them to this version once the upload issue is resolved. Supplemental data and resources for "Identifying non-coding variant effects at scale via machine learning models of cis-regulatory reporter assays" Including: MPAC and comparison model predictions for: Siraj 2026 (UKBB/BBJ/GTEx) MPRA (Supplementary Dataset 1) DNase allele specific effects (Supplementary Dataset 2) ClinVar (20260104) (Supplementary Dataset 3) COSMIC (v98) (Supplementary Dataset 4) GWAS tag SNVs + LD variants (Supplementary Dataset 6) Haplotype analyses (Supplementary Dataset 7) gnomAD (v3.1.2 SNPs and and small indels) (Supplementary Dataset 8) Saturation mutagenesis of human promoters (Supplementary Dataset 9) Saturation mutagenesis ENCODE dELSs (Supplementary Dataset 12) Supplemental Tables for: Recurrent COSMIC v98 emVar candidate drivers (Supplementary Dataset 5) Promoter level function x constraint relationships (Supplementary Dataset 10) Functional enrichments for promoter level function x constraint relationships (Supplementary Dataset 11) GTEx phenocopying results (Supplementary Dataset 13) All promoter and dELS seqlets (Supplementary Dataset 14) Model hyperparameters (Supplementary Dataset 15) All MPAC model artifacts (Supplementary Dataset 16)Detailed descriptions for all predictions and supplemental tables can be found in 'File Descriptions.xlsx'