What is a SNP (Single Nucleotide Polymorphism)?

If you want to understand how your genes affect your health, you need to know what a SNP (single nucleotide polymorphism) is. The Rogue Scientist explains.

What is a SNP? SNP (pronounced Snip) stands for single nucleotide polymorphism, something that’s easier to understand than it sounds.

Back in the day, nobody outside the realm of scientific research probably knew (or cared about) what SNPs are. But ancestry sites like 23andMe changed all that.

Your genome, something previously only accessed with the aid of a lab scientist or doctor, often at significant cost, became readily available for you to peruse. Now you can download a text file with the genotypes for half a million genetic markers.

Each one of these markers is a SNP.

More to the point, scientists have studied many of these SNPs for ages, including their potential impact on your health.

To understand how this works, it helps to know some basic genetics.

Genetic Variation 101

DNA provides the foundation of the human genome. The building blocks of DNA include four types of nucleotides:

T (Thymine)

A (Adenine)

G (Guanine)

C (Cytosine)

The DNA is organized into chromosomes: we have 46 (23 from Mom, 23 from Dad). Which means we have two copies of all our genes.

A gene is a specific segment of your DNA that codes for a protein. Everybody has the same genes, but we have different variants of those genes. Other terms for “variant” include allele, mutation, and polymorphism.

For example, we all have an eye color gene, but we have different variants of that gene, which gives us different eye colors. (In reality, eye color results from more than one gene, but you get the point.)

Our genomes have many kinds of polymorphisms, but SNPs are the most common (and most studied) because they’re easier and cheaper to genotype.

Single Nucleotide Polymorphisms (SNPs)

A SNP is a genetic variant involving only one DNA nucleotide.

To show you what a SNP looks like, let’s look at Gene X (a made-up example):

Person #1

ACGGTGCATGCACATG (Allele or Variant 1)

Person #2

ACGGGGCATGCACATG (Allele or Variant 2)

These two genes differ by one, and only one, nucleotide. Person 1 has a T while Person 2 has a G. We call this difference a SNP, or single nucleotide polymorphism.

Can changing only one nucleotide in your DNA make a difference? Yes. In some cases, it can make a dramatic difference.

H2 SNPs and Genotyping

When dealing with actual genetic data, like you get from 23andMe and similar sites, it will look a little different. Why? We have two copies of all genes (one from each parent).

Therefore, the picture for Gene X will look something like this:

Person #1


Person #2


For Gene X, Person #1 has the TG genotype for that SNP, while Person #2 has the GG genotype for that SNP. Your raw genetic data, such as what 23andMe gives you, will include this information.

SNPs, at least those used in research and on ancestry sites, have unique identifiers. The identifier usually begins with “rs,” followed by some numbers. Here’s a real sample from 23andMe:

From left to right, columns represent SNP ID, chromosome number, position on chromosome, and SNP genotype.

rs12564807     1          734462            AA

rs3131972       1          752721            GG

rs148828841   1          760998            CC

What Do SNPs Have To Do with Your Health?

If genes code for proteins, a small change in the structure of that gene can result in a change in that protein.

If the protein is an enzyme, the enzyme may work more (or less) efficiently depending on which version gets created. Or, if the SNP occurs in a tumor suppressor gene, it may affect that gene’s ability to do its job and prevent the formation of a tumor.

Lots of research has focused on many SNPs for their impact on all sorts of health conditions, including heart disease, specific cancers, and mental conditions such as depression and schizophrenia.

This knowledge can prove helpful when dealing with enzyme-mediated food sensitivities, such as lactose intolerance and tyramine intolerance. Certain genotypes are more likely to produce too little enzyme (or too slow an enzyme), which can impair your body’s ability to break down certain foods. 

However, when you look over your SNPs and 23andMe tries to estimate your chances of having a disorder or getting it in the future, remember two things:

  1. DNA can only do so much. Epigenetics (the regulation and expression of genes) has a lot more impact on your health, which you can read more about here. And epigenetic processes depend heavily on lifestyle, which can have a dramatic impact on your health, regardless of your DNA.
  2. Some conditions and diseases can result from having specific genetic variants. But more often, it’s the combination of many, many genes, plus lifestyle, that increases risk for disease.  

Despite these limitations, exploring your SNPs can be interesting. I’ll devote some future articles to this topic.  

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The Rogue Scientist

Christie Hartman is a writer and scientist specializing in science-based health. A biology major as an undergrad, she completed her PhD in behavioral genetics at the University of Colorado Boulder. Before starting her writing career, she worked as a scientist and professor at CU’s School of Medicine, where she studied the genetic contributions to substance abuse and antisocial behavior.

1 thought on “What is a SNP (Single Nucleotide Polymorphism)?”

  1. please help me understand if this is good dna or just average every kind of regular….. these are the first top sets that I need to learn more about… i have a few thousand pages to my dna

    rs3131972 1 752721 G G
    rs114525117 1 759036 G G
    rs4040617 1 779322 A A
    rs141175086 1 780397 C C
    rs115093905 1 787173 G G
    rs11240777 1 798959 G G
    rs6681049 1 800007 C C
    rs4422948 1 835499 A A
    rs57494724 1 837192 A A
    rs4475691 1 846808 C C

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