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Nutrigenomics of Vitamins + SNPs, Food Sources

Written by Ana Aleksic, MSc (Pharmacy) | Reviewed by Nattha Wannissorn, PhD (Molecular Genetics) | Last updated:

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Genetics can influence nutrient and vitamin levels, while nutrients can also affect gene expression. That’s where nutrigenomics and nutrigenetics come in – new sciences exploring the interplay between each person’s unique genetic makeup and their nutrition. Read on to learn more and to understand how it’s possible to adjust your nutrient intake to your unique DNA.

What Is Nutrigenomics?

The term nutrigenomics was first coined less than 10 years ago.

The terms nutrigenomics and nutrigenetics are often used interchangeably, although they don’t mean quite the same thing.

The Difference Between Nutrigenetics and Nutrigenomics

Genetics can have a profound influence on the way our bodies use nutrients. Our genes impact how nutrients are absorbed, transported, activated, and eliminated in the body.

  • Nutrigenetics is the science of how genetic variations influence a person’s nutritive status. It’s directly tied to how your DNA influences your vitamin and mineral levels and whether you are at risk for deficiencies. It can tell you if you should increase certain foods in your diet or take supplements to achieve optimal nutrient levels.

Genetic variations ———–> Nutritive status (vitamin and mineral levels)

Recommended daily allowances you see on most supplements, foods, and even when you go to the doctor are in no way adapted to your individual DNA. Some people may be predisposed to low B12, folate, or iron. Others may not absorb vitamin C as well. Nutrigenetics can match the nutrients you consume to your genetic makeup to establish a healthy balance in the body [1].

  • Nutrigenomics focuses on how nutrients and food can impact gene expression. It focuses on the interactions between nutrients and genes, especially when it has to do with disease prevention [2]. For example, nutrients such as vitamins or minerals from foods can activate or deactivate genes linked to risk for Alzheimer’s disease, heart disease, or other health issues. It could be represented as:

Nutrients (vitamins and minerals)  ———–> Gene expression/activity

Any kind of malnutrition — a nutrient deficiency or excess in your diet – can affect gene expression.

Effects on gene expression are known as “epigenetic” influences – each environmental factor that can turn our genes “on” or “off” is considered epigenetic. “Epi” means “on top of”, describing an influence “on top of genetics”. Methylation is a chemical modification that usually turns genes off (with some exceptions). A deficiency in methyl donors (such as folate, vitamin B12, choline, and methionine) can hinder the methylation process. Nutrigenomics deals with these epigenetic influences of diet and nutrients [1].

And although these terms are different, one can’t do without the other.

Nutrigenetics <———–> Nutrigenomics

The goal of both nutrigenetics and nutrigenomics is to match each individual’s genetic makeup to the diet and nutrient recommendations that would lead them to optimal nutrient levels and lowest overall disease risk.

How Do SNPs Influence Nutrients?

Single nucleotide polymorphisms (SNPs) are the most common type of variation in our DNA. They affect just one single letter in a gene that may be thousands of letters long. Over 10 million SNPs are currently known.

However small these “single letter variations” may seem, some SNPs can have a big influence on the activity of a gene.

If a SNP reduces the activity of a gene that makes a vitamin A-activating enzyme, then the person with this variation in their DNA will be at risk for low vitamin A levels.

A couple of SNPs in the MTHFR gene (we mention them below) can reduce the activity of the MTHFR enzyme and cause low levels of folate and other vitamins along with high homocysteine levels.


There are 13 known vitamin groups. Vitamins are small nutrients that broadly influence overall health, brain function, heart health, blood glucose levels, and energy production. The largest vitamin group is the vitamin B family, which has 8 subtypes.

Our body can create some vitamins, such as vitamin D and K2. But we have to rely on our diet to obtain most other vitamins, or alternatively on supplements.

Individual genetic variations can influence the effect vitamins will have on our body. The genes in our DNA control how vitamins are taken up, used, and eliminated. Certain SNPs can lead to decreased vitamin availability, and in some cases, deficiency [3, 4].

Vitamin A

Vitamin A refers to retinol (active vitamin A), retinal, retinoic acid, and provitamin A (carotenoids). Vitamin A is required a healthy brain, immune system, skin, teeth, eyes, bones, and the production of hormones [5].

This vitamin plays a diverse role, about which you can read in detail here. To summarize, vitamin A is important for the following [5, 6, 7]:

Vitamin A deficiency is the most common cause of preventable blindness in children globally. Additionally, vitamin A deficiency is linked to [6, 8, 9]:

  • Reduced immune system function and increased risk of infections
  • Diarrhea
  • Increased risk of complications in pregnant women
  • A buildup of glucose in the blood and possibly weight gain.

On the other hand, too much Vitamin A can reduce bone density because it competes with the uptake of other vitamins such as vitamin D and K2 [10].

Vitamin A Nutrigenetics

A vast number of proteins are involved in making and using vitamin A. Proteins that break down and take up vitamin A in the gut influence the amount of available vitamin A [11].

Beta-carotene is the main source of vitamin A in plants. It is converted in the body into the active form of vitamin A, which is affected by the activity of the BCO1 gene. SNPs in BCO1 can impact how well we utilize vitamin A from plant-based sources.

The following are a few SNPs associated with decreased BCO1 activity, resulting in lower levels of available vitamin A in the body [12, 13]:

Vitamin B

8 water-soluble vitamins make up the B-vitamin group. These vitamins play a role in the body’s energy system and are important for brain function. They are needed for [14]:

  • Cognitive Function
  • Memory
  • Mood
  • Production of multiple neurotransmitters
  • Energy production
  • Protein functioning and repair

Numerous clinical studies have unraveled the mechanisms and benefits of vitamins B9 and vitamin B12, especially when it comes to MTHFR mutations [14].

Vitamin B9 (Folate)

Vitamin B9 is commonly known as folate. It is inactive before the body converts it into methyl-folate. Vitamin B9 plays a major role in the synthesis and repair of DNA and amino acids, ensuring cellular proteins are functioning at full capacity. It also aids cell repair after exposure to damage. Folate is beneficial for [15]:

  • Pregnancy and fetal health
  • Reduction of cancer risk
  • Brain health and cognitive function
  • Antioxidant defense
  • Red blood cell production
  • Helping with depression
  • Proper immune function

Folate deficiency has been linked to anemia and neural tube defects in babies. However, supplementing folate may mask a vitamin B12 deficiency [15, 16].

You can read more about the health benefits of folate in detail here.

Vitamin B9 (Folate) Nutrigenetics

Vitamin B9 needs to be “activated” to l-methylfolate by a number of proteins to achieve its health benefits. Enzymes and proteins that play a role in this process include MTHFR and MTHFD1.

Variations in the MTHFR gene may reduce the activity of the enzyme MTHFR, and in turn, decrease the amount of available l-methylfolate. These variations, or SNPs (single nucleotide polymorphisms), are:

To take a deeper dive …

First, take a look at your genotype for rs1801133:

  • MTHFR CC677 (rs1801133) or GG is normal
  • MTHFR C677T (rs1801133) or AG may reduce MTHFR function by 30% maximum (not so bad)
  • MTHFR 677TT (rs1801133) or AA may reduce MTHFR function by up to 70% maximum (bad)

So if you see “AA” in your file, this means your MTHFR enzyme activity is more likely not to function as well. AG means it may have reduced function, but the chances are lower. And finally, GG is the normal version.

Next, take a look at rs1801131. This SNP has less of an effect on MTHFR function, but can still be useful to look at. For this SNP:

  • MTHFR AA1298 (rs1801131) or TT is normal
  • MTHFR A1298C (rs1801131) or GT may slightly reduce MTHFR activity (not so bad)
  • MTHFR 1298CC (rs1801131) or GG may reduce MTHFR activity more (bad)

To get a complete picture, look at your genotype for these SNPs together. If you have the “bad” genotype for both, your MTHFR enzyme is less likely to work well. The MTHFR 677TT/ rs1801133 AA and MTHFR 1298CC/rs1801131 GG combination can decrease MTHFR function the most.

Vitamin B12

Vitamin B12, also known as cobalamin, plays a large role in energy production, DNA synthesis, the formation of red blood cells, and is important for the insulation of brain cells. B12 has often been referred to as the “painkilling vitamin”.

Vitamin B12 may have benefits for [17, 14]:

  • Pain relief
  • Brain health and cognitive function
  • Depression
  • Improving sleeping patterns
  • Skin health
  • Reducing inflammation

Vitamin B12 deficiency may cause [17]:

  • Fatigue
  • Lethargy
  • Depression
  • Poor memory
  • Headaches

You can read about the detailed function and benefits of vitamin B12 here.

Vitamin B12 Nutrigenetics

Vitamin B12 absorption is dependent on enzymes and the good bacteria in the gut.

FUT2 is a protein that is elevated in the presence of healthy gut bacteria. It helps bacteria in our gut to increase vitamin B12 absorption. The following SNPs have been associated with increased absorption of vitamin B12 [18, 19, 20]:

If You Have MTHFR Mutations

If you have lower MTHFR function, supplement with 1 – 2 caps Methyl Guard Plus

Taking in the active forms of vitamins, methylcobalamin (vitamin B12) and methylfolate, reduces homocysteine levels. Bioavailable forms of vitamins do not need to be processed in the body and can be absorbed quickly [21].

Vitamin B6 and phosphatidylserine can also be used to divert homocysteine to cystathionine, preventing high levels of homocysteine. You might want to get your homocysteine levels measured. This is easily done with a blood test that you can ask for from your doctor.

Vitamin K

The term vitamin K refers to a group of fat-soluble vitamins that are found in two forms: phylloquinone, commonly known as vitamin K1, and menaquinone, also known as vitamin K2 [22, 23].

Our diet usually contains much more Vitamin K1, which constitutes 75% of vitamin K consumed. Vitamin K1 is found in plants, such as green leafy vegetables. Vitamin K2 is produced by our gut bacteria from vitamin K1. Plants can’t make vitamin K2, so the main dietary sources are animal-based (such as meat, butter, lard, and egg yolk) [23].

Vitamin K1 helps with blood clotting, whereas vitamin K2 also affects blood vessels, bone health, and cognition[24, 23].

To sum it up, vitamin K2 is beneficial for [24, 23, 22, 25]:

  • Bone health
  • Calcium absorption
  • Acts together with vitamin D
  • Cell growth
  • Reducing Inflammation
  • Energy production and mitochondrial health
  • Blood vessels
  • The heart

Vitamin K deficiency has been linked to osteoporosis and an increased risk of bone fractures. Also, vitamin K deficiency may result in increased blood clotting time, putting people at higher risk of bleeding [22, 24].

Supplementing vitamin K may help reduce the risk of heart disease, osteoporosis, diabetes, and arthritis [23].

Vitamin K2 (menaquinone) has many health benefits, about which you can read more here.

Vitamin K Nutrigenetics

Since vitamin K plays a critical role in blood clotting, many proteins can influence how well it functions. For blood clotting to start, vitamin K must be activated by an enzyme called VKORC1. The following SNPs have been linked to decreased levels of vitamin K in the body [26, 27]:

Side Effects of Vitamin Supplementation

Generally, the regular consumption of vitamins A, B9, B12, and K is considered safe and poses a low risk of harm. Very high doses these vitamins can have adverse effects [15, 16, 22].

High doses (above 3 mg) of active vitamin A (retinol) pose a risk of a condition known as hypervitaminosis A, which may result in [28]:

  • Dizziness
  • Nausea
  • Headaches
  • Skin irritation
  • Coma, and even death

Vitamin B12 has a very low potential for toxicity. No adverse effects have been noted [17].

However, high doses of vitamin B9 (folate) have been linked to neurological defects in people with megaloblastic anemia, which is caused by vitamin B12 deficiency [15].

Supplementing vitamin K is safe and side effects are rare [22].

Limitations and Caveats

Although extensive research has been conducted on the potential benefits and risks of vitamins, there is conflicting evidence regarding the effects of supplementing vitamins.

The long-term effects of using multivitamin supplements are unknown. In general, we recommend getting your vitamins from a balanced diet rather than from supplements, if possible.

Drug-Vitamin Interactions

Vitamin A (retinol) may interact with [6]:

  • Orlistat (Alli)
  • Psoriasis medication acitretin
  • Anti-cancer drug bexarotene

Vitamin B9 (folate) could possibly interact with [15]:

  • Rheumatoid arthritis medication sulfasalazine
  • Chemotherapy drug methotrexate
  • Anti-seizure drugs, such as phenytoin, carbamazepine, valproate

Vitamin B12 may interact with [17]:

  • Antibiotic chloramphenicol
  • Antacids reduce absorption by lowering the amount of hydrochloric acid, such as
  • Diabetes medication metformin

Vitamin K may increase or decrease the effects of a number of substances. Some substances can also decrease the absorption of vitamin K.

Vitamin K interacts with the following substances, resulting in either reduced activity of the drug or absorption of vitamin K. Consult your doctor if you are taking any of the following medication and are supplementing vitamin K [29, 22]:

  • May reduce the blood-thinning effects of warfarin
  • Orlistat (Alli) is an obesity medication. Taking Alli may reduce vitamin K absorption in the gut.
  • Antibiotic use may reduce vitamin K levels
  • Low-fat diets
  • Cholesterol-lowering drugs

Natural Sources of Vitamins

Although genetic variation plays a role in determining your vitamin levels and may contribute to deficiencies, the healthiest way to boost your vitamin levels is to ensure your take in these vitamins through your diet.

Food Sources of Vitamin A (retinol) and provitamin A (carotenoids)

Foods rich in active vitamin A (retinol) [30]:

Provitamin A (carotenoids) can be found in plant sources [7].

  • Mangoes
  • Papayas
  • Carrots
  • Dark leafy greens (spinach)

Food Sources of B Vitamins

Vitamin B9 (folate) [31, 32]:

  • Broccoli
  • Liver
  • Okra
  • Spinach
  • Poultry and meats
  • Eggs

Vitamin B12 [33, 17]:

  • Fish
  • Meat
  • Poultry
  • Eggs

Food Sources of Vitamin K1 and K2

Vitamin K1 (phylloquinone) [23]:

  • Spinach
  • Broccoli
  • Iceberg lettuce
  • Vegetable oils

Vitamin K2 (menaquinones) [23]:

  • Meat
  • Eggs

Find Out Your Nutrigenomics with SelfDecode’s Vitamin DNA Wellness Report

Your genes play a huge role in determining your vitamins levels and activity. Ensuring you get the specific nutrients you need is essential for living at your best.

Find out your genetic tendency that may affect your absorption, metabolism, usage, and elimination of vitamins through SelfDecode’s Vitamin DNA Wellness Report. The report curates the most important vitamin-related SNPs from your genome file, interprets what they mean for your health, and provides recommendations to address the health risks.

SelfDecode is a sister company of SelfHacked. The proceeds from your purchase of this product are reinvested into our research and development, in order to serve you better. Thank you for your support.

About the Author

Ana Aleksic

MSc (Pharmacy)
Ana received her MS in Pharmacy from the University of Belgrade.
Ana has many years of experience in clinical research and health advising. She loves communicating science and empowering people to achieve their optimal health. Ana spent years working with patients who suffer from various mental health issues and chronic health problems. She is a strong advocate of integrating scientific knowledge and holistic medicine.

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