single-nucleotide polymorphism

Any two unrelated people share almost all of their DNA — about 99.9 percent of it is identical. The differences that make us individuals are scattered through the remaining sliver, and the most common kind is wonderfully simple: at a particular spot in the genome, some people carry one letter and others carry a different one. Where I have a C, you might have a T. That single-letter difference, when it is common enough in the population, is a single-nucleotide polymorphism, or SNP.

Precisely, a SNP is a position in the genome where a single base differs between individuals and where the rarer version is common enough to count as a normal variant rather than a private mutation (a rough convention is at least 1 percent of the population). There are tens of millions of SNPs catalogued in humans, dotted roughly every few hundred bases. Most fall outside genes or in places where the change is silent, so they do nothing noticeable; a minority sit where they alter a protein or a regulatory signal and can subtly affect a trait. Because nearby SNPs tend to be inherited together in blocks, measuring a handful can stand in for a whole region.

SNPs are the workhorse markers of human genetics. They are what GWAS scans, what ancestry and forensic tests read, and what direct-to-consumer genotyping chips report. But two honest points matter. First, the vast majority of SNPs are harmless variation — the raw material of human diversity, not defects; calling a SNP a 'risk variant' usually means it nudges a probability slightly, not that it dooms anyone. Second, because SNPs travel in linked blocks, an associated SNP is frequently just a flag near the truly responsible change, not the change itself — the same caution that haunts GWAS.