A single nucleotide polymorphism, or SNP (pronounced “snip”), represents the most common type of genetic variation found among people. These differences are a change in a single DNA building block, known as a nucleotide, at a specific position in the genome. While the vast majority of human DNA is identical, SNPs account for the tiny variations that make each individual genetically unique. Understanding these genetic markers provides insight into human biology, from determining physical traits to predicting disease risk.
Defining Single Nucleotide Polymorphisms
A single nucleotide polymorphism is defined by the substitution of one base pair—adenine, thymine, cytosine, or guanine—at a specific location. This change is considered a polymorphism only if it occurs in at least one percent of the population; a rarer change is classified as a single-nucleotide variant or a mutation.
These markers are frequent across the human genome, occurring roughly once every 300 to 1,000 base pairs. An average person carries between four and five million SNPs, making them the primary source of genetic diversity. Most SNPs are located in intergenic regions (between genes) or within non-coding regions, such as introns.
SNPs are found in both coding regions (instructions for proteins) and non-coding regions (regulating gene activity). A coding SNP can be synonymous (silent), meaning the change does not alter the resulting amino acid, or non-synonymous, meaning it changes the amino acid or introduces an early stop signal. Non-coding SNPs influence gene expression by acting as switches that turn genes on or off.
How SNPs Drive Human Biological Variation
SNPs are responsible for the differences between individuals. These genetic markers are the foundation of human biological variation, influencing a wide range of observable traits, known as phenotypes. Alterations in the DNA sequence translate into differences in how genes are expressed or how proteins function.
For instance, SNPs in the OCA2 and HERC2 genes are associated with variations in eye color. Hair texture is influenced by multiple SNPs that affect the structure of hair follicles. Height is a complex trait determined by the combined effect of hundreds of different SNPs scattered throughout the genome.
SNPs can also influence sensory perception, such as the ability to taste certain bitter compounds. A specific SNP in the TAS2R38 gene determines whether an individual perceives the bitter taste of compounds like phenylthiocarbamide (PTC). These variations demonstrate that SNPs are drivers of the natural spectrum of human traits.
SNPs and Their Role in Disease Risk and Drug Response
SNPs have profound medical implications, playing a significant role in susceptibility to complex diseases and response to medications. Common diseases like Type 2 diabetes, heart disease, and Alzheimer’s are linked to the cumulative effect of many different SNPs, each contributing a small amount to the overall risk.
Specific SNPs can affect the function of genes involved in metabolic pathways, inflammation, or cell signaling, increasing or decreasing a person’s lifetime risk for a condition. For example, variations in the APOE gene, specifically the \(\epsilon4\) allele, are strong predictors of increased risk for late-onset Alzheimer’s disease. Researchers use this information to identify individuals who may benefit from early screening or preventative lifestyle changes.
The field of pharmacogenomics focuses on how an individual’s genetic makeup influences their response to drugs. SNPs in genes that encode drug-metabolizing enzymes dictate how quickly a medication is processed and eliminated, affecting both efficacy and toxic side effects. Variations in the CYP2D6 gene determine how a patient metabolizes common antidepressants and pain medications. Testing for these SNPs allows healthcare providers to personalize drug dosage.
Utilizing SNPs in Genetic Research and Ancestry Mapping
The analysis of SNPs enables scientists to explore the genetic basis of traits and diseases. The Genome-Wide Association Study (GWAS) is a powerful tool that scans the genomes of thousands of individuals to find SNPs statistically associated with a particular trait or disease. GWAS compares the frequency of millions of SNPs between groups (e.g., people with a disease and healthy controls) to pinpoint linked genomic regions.
SNPs are also the foundation of consumer ancestry testing services. These companies analyze an individual’s unique pattern of hundreds of thousands of SNPs and compare them to reference databases of known populations. By identifying shared SNP patterns, or haplotypes, the services can trace the geographic origins and migration history of a person’s ancestors. This application demonstrates how common genetic markers can reveal deep connections to human history.