This dataset contains the processed data used in the analyses of the paper: “Linking Genetic Risk to Disease-Relevant Cellular States via Metacell-Informed Modeling with ICePop” (https://doi.org/10.64898/2026.04.01.715877). Code and notebooks to reproduce the analyses are available at: https://github.com/krishnanlab/icepop_analysis The ICePop Python package is available at: https://github.com/krishnanlab/icepop_public This dataset includes the following components: simulation.tar.gz Input data for causal and null simulation studies. magma.tar.gz MAGMA-derived z-scores for all diseases/traits analyzed in this study. Corresponding disease/trait metadata are provided in Supplementary Data 1. TM_FACS.tar.gz Processed single-cell RNA-seq data from Tabula Muris (FACS). Raw data were obtained from: https://doi.org/10.6084/m9.figshare.5829687.v7 mouse_colon.tar.gz Single-cell RNA-seq data of mouse colon enteric cells from Drokhlyansky et al. Cell 2020. Raw data were obtained from the Single Cell Portal (SCP1038). This archive also includes SFARI gene scores downloaded from https://gene.sfari.org/database/human-gene/