As part of the National Cancer Institute's Cancer Genome Anatomy Project (CGAP) the Genetic Annotation Initiative (GAI) is attempting to expand the collection of gene-based genetic analysis reagents for cancer research. Using a set of sequence analysis tools, (the SNPpipeline) we have identified more than 30,000 high-probability "candidate" SNPs by examining publicly available expressed sequence tag (EST) chromatograms. PCR assays have been developed to validate a subset of these data. Using a pooled sample of 92 independent CEPH individuals, examined by MALDI-TOF mass spectrometry more than 7000 SNPs have been validated. The above approach has also been applied to mouse EST data. Using this data more than 16,000 candidate mouse SNPs have been identified. To present the genetic variants in a format useful for the human genetics community we have constructed an integrated genetic/physical SNP map based on the CHLC/ABI Prism linkage marker set. Genetic map positions of reference markers are from the CHLC; physical map positions are from the GeneMap'98 Genebridge4 radiation hybrid map. Tissue-specific and cancer-specific views of these maps are also available. These maps permit the selection of SNPs for genes with specific expression patterns. Through related CGAP infrastructure it is also possible to view the SNP data in other biologically relevant contexts. SNPs can be queried through the developing Gene Ontologies or through biologic pathways. These results have been integrated with those obtained from the TSC to give a comprehensive view of gene-based SNPs. A browser shows the location of each variant within the gene and provides information on whether the variant will result in a coding change. Motif models fit to the transcripts graphically indicate the location of functional characteristics of the gene. The significance of the variant's influence on the fit of these models is assessed and displayed. The integrated maps, a Java-based tool for viewing candidate SNPs in the context of EST assemblies, reagent information (including PCR primers and extension primers), and a SNP search engine are available at our website: http://cgap.nci.nih.gov. We provide access to our SNP detection software for non-commercial use.