Genotype data from UK Biobank are available through the UK Biobank data access process (http://www.ukbiobank.ac.uk/register-apply/). GTEx v7 Adipose tissue dataset gene prediction models (http://gusevlab.org/projects/fusion/). Publicly available summary statistics for LDL, SBP and IBD were obtained from the IEU OpenGWAS project (https://gwas.mrcieu.ac.uk/) using GWAS IDs ‘ukb-d-30780_irnt’ (LDL), ‘ukb-a-360’ (SBP) and ‘ebi-a-GCST004131’ (IBD). Publicly available summary statistics for SCZ from the Psychiatric Genetics Consortium and the CardiffCOGS study were obtained from http://walters.psycm.cf.ac.uk/. Publicly available prediction models for 49 GTEx tissues from PredictDB (https://predictdb.org/post/2021/07/21/gtex-v8-models-on-eqtl-and-sqtl/).

Our software is available at https://xinhe-lab.github.io/ctwas/. Code related to analyses performed in this study can be accessed at https://github.com/xinhe-lab/ctwas-paper and https://zenodo.org/doi/10.5281/zenodo.10373122.

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