Provided is a method of identifying a candidate gene for a genetic disease includes obtaining a disease network, disease-gene association information, and a gene network, obtaining a single nucleotide polymorphism (SNP) network based on intra-relation data between a plurality of SNPs, and inter-relation data between genes and SNPs, creating a disease-gene-SNP multilayered network based on the disease network, the disease-gene association information, the gene network, the SNP network, and the interrelation data between genes and SNPs, and identifying a candidate gene for a genetic disease using the multilayered network.