Vitamins & Micronutrients

Reduces beta-carotene conversion to vitamin A (retinol) by ~32% per T allele, contributing to "poor converter" status for plant-based vitamin A

Reduces beta-carotene to retinol (vitamin A) conversion efficiency, contributing to the "poor converter" phenotype

Intergenic GWAS tag SNP near the BCO1 pathway, associated with circulating beta-carotene and retinol levels independently of the functional BCO1 coding variants

Upstream regulatory variant that reduces BCO1 (BCMO1) catalytic activity by ~48%, independently limiting beta-carotene to vitamin A conversion; the top GWAS hit for circulating beta-carotene levels

Upstream regulatory variant near BCO1 that reduces beta-carotene to vitamin A conversion efficiency by approximately 59%

Alters vitamin D binding protein affinity, affecting total and bioavailable 25-hydroxyvitamin D levels

Vitamin D binding protein variant that determines VDBP isoform, affecting vitamin D transport, bioavailability, and supplementation response

Intronic GWAS tag variant in the vitamin D binding protein gene, the strongest common genetic determinant of circulating 25-hydroxyvitamin D levels

Influences vitamin D synthesis by regulating how much 7-dehydrocholesterol is available for conversion to vitamin D3 in the skin

Near-gene intronic variant in the DHCR7/NADSYN1 locus on chromosome 11 that tags lower circulating vitamin D3 synthesis capacity; a near-perfect proxy for the canonical vitamin D synthesis SNP rs12785878

Vitamin D receptor start codon variant — determines receptor protein length and transcriptional activity

Near-gene regulatory variant affecting vitamin D 24-hydroxylase expression — modulates the rate at which active vitamin D is degraded

Intronic NADSYN1 variant in the DHCR7/NADSYN1 vitamin D locus; T allele tags the lower-vitamin-D haplotype, reducing 7-dehydrocholesterol availability for skin vitamin D3 synthesis

Intronic NADSYN1 variant at the DHCR7/NADSYN1 vitamin D locus; A allele was the top GWAS hit for lower circulating 25-hydroxyvitamin D in Ahn et al. 2010 (P = 3.4×10⁻⁹), reducing 7-dehydrocholesterol availability for skin vitamin D3 synthesis

Transcobalamin II variant affecting cellular delivery of vitamin B12 via holotranscobalamin binding efficiency

Tag SNP in the NBPF3/ALPL locus on chromosome 1 — the strongest common genetic determinant of circulating vitamin B6 (PLP) levels, acting through alkaline phosphatase-mediated catabolism

Intronic variant near ALPL associated with increased alkaline phosphatase activity, lowering circulating PLP (the active form of vitamin B6) — those with two G copies have higher ALPL activity and lower plasma B6 levels

Missense variant in the FTCD enzyme that impairs one-carbon unit transfer from histidine catabolism into the folate pool, reducing arsenic methylation efficiency and increasing toxicity risk

Intronic CBS variant that tags the CBS locus in GWAS studies; associated with altered homocysteine metabolism capacity and one-carbon methylation efficiency

Primary intestinal and renal vitamin C transporter — variant reduces ascorbate absorption and reabsorption efficiency

Intronic variant in the SVCT2 tissue vitamin C transporter — associated with differences in plasma vitamin C levels in the EPIC cohort

Intronic variant in the tissue vitamin C transporter SVCT2 — GG homozygotes carry ~24% higher plasma vitamin C levels than AA homozygotes

Regulates expression of the alpha-tocopherol transfer protein, the key determinant of circulating vitamin E levels

Primary variant causing hereditary hemochromatosis type 1, disrupting iron regulation and hepcidin signaling

Second most common hereditary hemochromatosis variant, mildly increasing iron absorption and modestly raising iron stores

Master regulator of iron absorption via hepcidin control — the strongest common genetic determinant of iron status

Determines secretor status — whether ABO blood group antigens are secreted into bodily fluids, affecting gut microbiome, vitamin B12 levels, and infection susceptibility

Missense variant in the FUT2 fucosyltransferase enzyme that alters haptocorrin glycosylation and is one of the strongest genetic determinants of circulating vitamin B12 levels

Near-gene regulatory variant near FUT6 that reduces fucosyltransferase expression and lowers circulating vitamin B12 — especially common in Indians

Intronic regulatory variant in FUT6 that alters HNF4α binding and fucosyltransferase expression, influencing intestinal fucosylation and circulating vitamin B12 levels — especially relevant in South Asian populations

Missense variant in the major renal urate transporter; the Arg265 (C) allele is associated with less efficient urate excretion, elevating serum uric acid and gout risk, with the strongest effects in East Asian populations and in women

Intronic SLC2A9 variant tagging an independent urate-transport signal; the protective C allele (~26% global frequency) reduces serum uric acid by 0.23–0.46 mg/dL per copy — with a substantially stronger effect in women — and attenuates the hyperuricemic response to fructose; the major T allele confers elevated uric acid and increased gout risk, particularly in Europeans

Missense variant in the GLUT9 renal urate transporter; the T allele (Val→Ile substitution) reduces urate reabsorption in the proximal tubule, lowering serum uric acid and conferring protection against hyperuricemia and gout

Upstream regulatory variant in the URAT1 urate reabsorption transporter gene; the C allele increases SLC22A12 expression and renal urate reabsorption, elevating serum uric acid and gout risk, with the strongest effects in East Asian and African populations where the C allele predominates

Intronic variant in the OAT4 renal urate transporter that modulates uric acid reabsorption in the proximal tubule, with the C allele raising serum urate and increasing gout risk especially in diuretic users

Uromodulin promoter variant — strongest GWAS signal for chronic kidney disease risk, affecting salt handling and blood pressure via NKCC2

UMOD promoter variant affecting uromodulin expression, linked to CKD, salt-sensitive hypertension, and gout risk with paradoxical kidney stone protection

Rare AMPK beta-1 subunit variant linking central energy sensing to shared migraine and type 2 diabetes susceptibility

Intronic NOS3 variant that alters splicing factor binding and is associated with blood pressure and cardiovascular risk, with effects that are amplified by physical activity

Intronic NOS3 variant associated with ankle-brachial index and peripheral arterial disease risk in hypertensive adults; G allele linked to lower peripheral blood flow

Most common alpha-1 antitrypsin deficiency variant causing protein misfolding, lung disease, and liver disease