A tool for the gene-set (or pathway) analysis of a genome-wide association study result. It accepts a genome-wide list of SNPs and their association P-values. It summarizes the SNP P-values into nearby genes. The gene-by-gene summary results are then further summarized by gene-sets such as Gene Ontology, KEGG pathways, or user-created gene-sets. Various standardization and statistical tests can be performed and the resulting gene-sets that pass a significance level after multiple-testing correction are reported. The tool is written in Java and is available as a standalone version. It has been published as "Nam, D., Kim, J., Kim, S. Y. & Kim, S. GSA-SNP: a general approach for gene set analysis of polymorphisms. Nucleic Acids Res. 38 (Suppl. 2), W749–W754 (2010).