SNPs may also lead to premature termination of peptides (non-sense), which would disable the protein function. Each of these distinct functional effects may incur a risk that causes a disease. Therefore, to prioritize SNPs for the study of complex diseases, it is critical to identify the functional variants that are most likely to have functional effects leading to disease phenotypes before genotyping. Based on previous studies of the functional effects of polymorphisms, Tabor et al. (1) presented a prioritization strategy that associates the relative risk of a SNP with its location and the type of sequence variants. We extended their strategy with our recent findings and developed a decision tree to assess the risk of a SNP. The decision tree, shown in Figure 1, classifies a SNP into 1 of 13 types of the functional effects, each of which is assigned a risk ranking number between 0 and 5. A high risk rank implies a high-risk level. Table 1 gives the definitions of the function types, effects and their predicted risk ranking.
