DNA Traits · Heart & circulation

HDL cholesterol concentration association

The blood level of HDL cholesterol.

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Evidence · Replicated

What the research found

In the cited research, the T allele at rs173539 was associated with higher blood HDL cholesterol concentrations in the studied cohorts.

CC: Lower average
CT: Middle
TT: Higher average

Modest effect

What the study found

In the study, each copy went with higher HDL cholesterol on average.

Framingham Heart Study participants (second and third generation, European ancestry) · Table 2 (FHS effect size column, footnotes a and b)

Evidence: Genome-wide association at an established lipid locus
Who was studied: European-ancestry participants across multiple research cohorts

1000 Genomes Project

How common each genotype is

How common each genotype is in the 1000 Genomes Project, by region
Region	CCLower average	CTMiddle	TTHigher average
All regions2,504 people	46%	41%	12%
Africa661 people	36%	45%	19%
The Americas347 people	49%	38%	12%
East Asia504 people	59%	36%	6%
Europe503 people	50%	41%	9%
South Asia489 people	42%	45%	13%

Among the 2,504 people of the 1000 Genomes Project, in five world regions. These percentages describe groups of people, never anyone’s chance of having a trait.

Ancient genomes

Through time

How often the studied letter was read in ancient people, era by era, in the region chosen.

Region

Through time: Europe
Before farmingbefore 6500 BC	19%7 of 36 copies read
First farmers6500 to 3000 BC	20%79 of 403 copies read
Bronze Age3000 to 1200 BC	23%68 of 299 copies read
Iron Age and Antiquity1200 BC to AD 600	30%137 of 455 copies read
Middle AgesAD 600 to 1500	30%111 of 366 copies read
Today1000 Genomes	30%300 of 1,006 copies

Neanderthal and Denisovan genomes

Altai Neanderthal: No copies
Vindija Neanderthal: No copies
Chagyrskaya Neanderthal: No copies
Denisovan: No copies

For most ancient people only one of their two copies can be read, so these counts are copies read, not people. Close relatives, repeated samples and samples the archive marks as unreliable are left out. Damage in old DNA can fake this letter, so it is counted only from samples treated to remove that damage and from high-quality genomes. Ancient genomes from the Allen Ancient DNA Resource (AADR v66): 15,136 people.

rs173539

The marker

Gene or region: CETP region
Marker: rs173539
Location: Chromosome 16 · GRCh37 56,988,044 · GRCh38 56,954,132
Letters studied: C and T, with T as the studied allele

A DNA Traits report reads this marker in your raw DNA file and shows which of the three genotypes is yours, with how common it is. It counts the copies of the studied allele; it does not measure the trait itself.

Marker: CETP region · rs173539
Location: Chromosome 16 · GRCh37 56,988,044 · GRCh38 56,954,132
Studied allele: T
Published statistic: beta +0.25 SD per T allele (SE 0.02) in FHS; combined stage 1 P 4e-75, N 19,794; Table 2; 0.25 SD per copy (Table 2 (FHS effect size column, footnotes a and b))
1000 Genomes Project phase 3, people with 0, 1 and 2 copies: All regions 1159 / 1038 / 307 · Africa 239 / 296 / 126 · The Americas 171 / 133 / 43 · East Asia 296 / 180 / 28 · Europe 249 / 208 / 46 · South Asia 204 / 221 / 64

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Limits

What it cannot tell you

This is an association with a blood lipid measurement, not an estimate of your current lipid level. A single marker is not a test for high cholesterol, cannot predict heart attack or stroke risk and does not guide diet, medication or treatment. Only the studied C/T allele pair is interpreted.

Common variants at 30 loci contribute to polygenic dyslipidemia (Kathiresan et al., 2009)

The same topic

More in Heart & circulation

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