DNA Traits · Heart & circulation

HDL cholesterol, LIPG marker

The blood level of HDL cholesterol.

See a sample report

Free, once per account. Your own private report.

Evidence · Replicated

What the research found

In the cited research, the T allele at rs4939883 was associated with lower blood HDL cholesterol concentrations in the studied cohorts.

CC: Higher average
CT: Middle
TT: Lower average

Modest effect

What the study found

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

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

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	CCHigher average	CTMiddle	TTLower average
All regions2,504 people	59%	33%	9%
Africa661 people	25%	50%	25%
The Americas347 people	76%	22%	2%
East Asia504 people	63%	33%	4%
Europe503 people	69%	28%	3%
South Asia489 people	76%	21%	3%

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	39%16 of 41 copies read
First farmers6500 to 3000 BC	13%63 of 483 copies read
Bronze Age3000 to 1200 BC	19%62 of 328 copies read
Iron Age and Antiquity1200 BC to AD 600	16%90 of 566 copies read
Middle AgesAD 600 to 1500	17%64 of 372 copies read
Today1000 Genomes	17%171 of 1,006 copies

Neanderthal and Denisovan genomes

Altai Neanderthal: 2 copies
Vindija Neanderthal: 2 copies
Chagyrskaya Neanderthal: 2 copies
Denisovan: 2 copies

Neanderthals and Denisovans carried this letter too: it is the older of the two.

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.

rs4939883

The marker

Gene or region: LIPG region
Marker: rs4939883
Location: Chromosome 18 · GRCh37 47,167,214 · GRCh38 49,640,844
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: LIPG region · rs4939883
Location: Chromosome 18 · GRCh37 47,167,214 · GRCh38 49,640,844
Studied allele: T
Published statistic: beta -0.14 SD per T (SE 0.02) in FHS; combined stage 1 + 2 P 7e-15, N 19,785 (Table 2). Hoffmann 2018: T -0.064, P 2e-45; Graham 2021: C +0.095, P 6e-19 (GWAS Catalog); 0.14 SD per copy (Table 2 (FHS effect size column))
1000 Genomes Project phase 3, people with 0, 1 and 2 copies: All regions 1468 / 821 / 215 · Africa 167 / 331 / 163 · The Americas 263 / 78 / 6 · East Asia 320 / 166 / 18 · Europe 347 / 141 / 15 · South Asia 371 / 105 / 13

See this card in the sample report

Limits

What it cannot tell you

LIPG makes endothelial lipase; the marker reads the amount of HDL cholesterol in blood, not how HDL particles work.

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

The same topic

More in Heart & circulation

Free, once per account

See your own two letters.

Upload the raw DNA file you already have. Your report reads this marker and every other card studied for you, each with its evidence and its limits.

See a sample report