Variation module integrates genetic variations, phenotype and transcription data of the B. napus population, providing variation query and association between genotype and phenotype in mining candidate variations/genes old traits. There are three functional interfaces in Variation module, including Single-locus model, Multiple-locus model and Customized phenotype. Information about variations, including annotation, allele frequency, distribution, description of gene expression and phenotypic values, are provide in Single-locus model, enabling user to screen candidate variations/genes of traits. Multi-locus model enables users to combine the multiple loci cross genes to check gene-gene interactions and their contribution to phenotype. In Customized phenotype, users can upload their own phenotype data to inspect the candidate variations/genes of traits. Users can use these functions based on Darmor or ZS11 reference genome.