What you carry at this position in your DNA and what research says about it.
Cholesterol Levels: 10/10 evidence, 14 publications.
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Sample genotype (not yours): C/C
Typical Cholesterol and Lipid Levels
Baseline levels of HDL and LDL cholesterol are typical for the general population. There is no genetically lowered risk or elevated risk for metabolic syndrome from this variant.
What this genotype means: Typical circulating HDL and LDL levels; Baseline risk for metabolic syndrome.
Sample genotype (not yours): C/T
Favorable Cholesterol and Lipid Profile
Presence of one protective T allele is linked to higher HDL cholesterol and lower triglycerides. This profile supports a healthier cardiovascular baseline.
What this genotype means: Moderately higher HDL cholesterol; Slightly lower LDL and triglycerides.
Sample genotype (not yours): T/T
Optimal Cholesterol and Lipid Profile
Presence of two protective T alleles is linked to significantly higher HDL cholesterol and lower triglycerides. This genetic profile provides strong natural support for cardiovascular health.
What this genotype means: Significantly higher HDL cholesterol; Noticeably lower LDL and triglycerides.
Gene function and biological role
Gene Function: The CETP gene encodes cholesteryl ester transfer protein, a key regulator of lipid metabolism in the bloodstream [1]. This protein facilitates the exchange of cholesteryl esters from high-density lipoprotein (HDL) to very-low-density lipoprotein (VLDL) and low-density lipoprotein (LDL) [1]. Through this process, CETP plays a central role in reverse cholesterol transport, which clears excess cholesterol from peripheral tissues and delivers it to the liver [1]. Variations in this gene can significantly alter circulating levels of both protective HDL and atherogenic LDL particles [2]. Consequently, CETP is a major genetic determinant of cardiovascular health and a target for lipid-modifying therapies [3].
Variant Impact: Located in an intergenic region upstream of the CETP gene, rs173539 is a common single nucleotide polymorphism that influences gene expression [1]. This genetic variant lies within a large regulatory haplotype block that alters transcription factor binding sites in liver tissue [1]. The change from a cytosine (C) to a thymine (T) allele is strongly associated with reduced CETP expression and activity [1]. Lower CETP activity slows the transfer of cholesterol away from HDL particles, resulting in higher circulating levels of protective HDL [2]. This functional impact makes the variant a key marker for polygenic lipid profiles and metabolic health [4].
Key Insight: This variant acts as a natural CETP inhibitor, mimicking the effects of modern cholesterol-lowering medications.
Location: CETP. Chromosome 16 · 16q13 · 57.0 Mb
Estimated prevalence by population
Global 44.5%; European 44.7%; African 39.5%; East Asian 58.0%; South Asian 38.9%; Americas 48.0%; Ashkenazi 52.5%; Finnish 51.9%; Middle Eastern 54.0%; Amish 34.7%.
Estimated CC genotype frequency.
Global 44.2%; European 44.3%; African 46.7%; East Asian 36.3%; South Asian 47.0%; Americas 42.5%; Ashkenazi 39.9%; Finnish 40.3%; Middle Eastern 39.0%; Amish 48.4%.
Estimated CT genotype frequency.
Global 11.2%; European 11.0%; African 13.8%; East Asian 5.7%; South Asian 14.2%; Americas 9.4%; Ashkenazi 7.6%; Finnish 7.8%; Middle Eastern 7.0%; Amish 16.9%.
Estimated TT genotype frequency.
Showing effects for C/C genotype
Cardiovascular & Metabolic
Lipids & Cholesterol
HDL Cholesterol. Evidence: 10/10. Source: PMID 19060906. Typical HDL.
LDL Cholesterol. Evidence: 9/10. Source: PMID 29507422. Typical LDL.
Triglycerides. Evidence: 10/10. Source: PMID 21386085. Typical Levels.
Metabolic Syndrome & Insulin Resistance
Metabolic Syndrome. Evidence: 8/10. Source: PMID 21386085. Typical Risk.
Showing effects for C/T genotype
HDL Cholesterol. Evidence: 10/10. Source: PMID 19060906. Higher HDL.
LDL Cholesterol. Evidence: 9/10. Source: PMID 29507422. Lower LDL.
Triglycerides. Evidence: 10/10. Source: PMID 21386085. Lower Levels.
Metabolic Syndrome. Evidence: 8/10. Source: PMID 21386085. Lower Risk.
Showing effects for T/T genotype
HDL Cholesterol. Evidence: 10/10. Source: PMID 19060906. Highest HDL.
LDL Cholesterol. Evidence: 9/10. Source: PMID 29507422. Lowest LDL.
Triglycerides. Evidence: 10/10. Source: PMID 21386085. Lowest Levels.
Metabolic Syndrome. Evidence: 8/10. Source: PMID 21386085. Lowest Risk.
What this genotype means for the people who carry it
Sample genotype: CC (Homozygous)
Two copies of the common C allele are associated with standard levels of circulating lipids [1]. Without the protective effects of the minor T allele, CETP protein expression remains at its typical baseline level [2]. This results in standard rates of cholesterol transfer from protective HDL to LDL and VLDL particles [2]. Consequently, circulating HDL cholesterol levels are typical, while LDL cholesterol and triglycerides remain at average population baselines [1]. Susceptibility to metabolic syndrome is also typical, reflecting standard genetic risk [3]. Maintaining a heart-healthy diet and regular exercise remains the primary way to support optimal lipid profiles.
Typical circulating HDL and LDL levels; Baseline risk for metabolic syndrome.
Sample genotype: CT (Heterozygous)
One copy of the minor T allele is associated with a favorable shift in blood lipid levels [1]. This genetic variation reduces the expression of the CETP protein, slowing down the clearance of protective HDL cholesterol from the bloodstream [2]. As a result, circulating HDL levels are typically higher than the population average [1]. Concurrently, levels of LDL cholesterol and triglycerides tend to be lower [1]. This combined lipid-lowering effect is associated with a reduced risk of developing metabolic syndrome [3]. The overall profile mimics mild genetic inhibition of CETP, offering a natural cardiovascular advantage.
Moderately higher HDL cholesterol; Slightly lower LDL and triglycerides.
Sample genotype: TT (Homozygous)
Two copies of the minor T allele are associated with the most pronounced favorable lipid profile at this locus [1]. With two protective alleles, CETP gene expression is significantly reduced, which preserves high levels of circulating HDL cholesterol [2]. This genetic profile leads to substantially higher HDL levels compared to the general population [1]. It also drives down levels of atherogenic LDL cholesterol and triglycerides [1]. These combined lipid improvements contribute to a significantly lower likelihood of metabolic syndrome [3]. This natural genetic setup provides robust, lifelong support for maintaining healthy arteries and cardiovascular resilience.
Significantly higher HDL cholesterol; Noticeably lower LDL and triglycerides.
Variants with shared genetic architecture
rs12720922 · CETP Gene · Chr 16 · Cholesterol and Heart Health
rs1532624 · CETP Gene · Chr 16 · Lipid Levels and Statins
rs17231506 · CETP Gene · Chr 16 · Cardiovascular Health
Common variants at 30 loci contribute to polygenic dyslipidemia.
A bivariate genome-wide approach to metabolic syndrome: STAMPEED consortium.
A large electronic-health-record-based genome-wide study of serum lipids.
Content updated August 2026.
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