We generated an input file for cMAGMA that is comparable to H-MAGMA. We used the same gene model (Gencode v26) and a SNP list used for H-MAGMA, and allowed a window of 35kb upstream and 10kb downstream of each gene as previously described16,52. Subsequently, any intronic and nearby intergenic SNPs were assigned to the genes based on positional mapping. This input file can be found in the github repository: https://github.com/thewonlab/H-MAGMA.
