Abstract: Visualization is an important part of genome data analysis. However, the size and diversity of data sets generated by today's sorting and array based analysis methods pose major challenges to current visualization tools. For this reason, comparing the advantages and deficiencies with existing visualization tools, a visualization system was designed to extract the significant information from the data of Genome-wide association study (GWAS) and combine this information with the brain image. It can generate a Heatmap Plot of information that the researcher is interested in. The data in the Heatmap Plot can display the Manhattan Plot for the corresponding phenotype and the phenotype information (different regions use different p-value for color rendering) in the Brain Image to the corresponding Single nucleotide polymorphism (SNP). This visualization system would provide the researcher more intuitive visualization.