SNPs are scattered throughout the genome and are found in both coding AND noncoding regions. SNPs can cause silent, harmless, harmful, or latent effects. They occur with a very high frequency, with estimates ranging from about 1 in 1000 bases to 1 in 100 to 300 bases. This means that there could be millions of SNPs in each human genome. The abundance of SNPs and the ease with which they can be measured make these genetic variations significant.

Most SNPs occur in noncoding regions and do not alter genes. Scientists are finding that some of these SNPs have a useful function. If a SNP is frequently found close to a particular gene, it acts as a marker for that gene.

The remaining SNPs occur in coding regions. They could alter the protein made by that coding region, which in turn could influence a person's health. To understand how a SNP could do this requires a brief look at proteins and their building blocks, amino acids.