Evidence · Replicated

What the research found

In the cited research, the A allele at rs3801387 was associated with lower lumbar-spine bone mineral density in the studied cohorts.

GG: Higher average
AG: Middle
AA: Lower average

Slight effect

What the study found

In the study, each copy went with lower lumbar-spine bone mineral density on average.

European-ancestry adults in the GEFOS Stage 2 replication cohorts · Table 1 (LS-BMD, Stage 2)

Evidence: Genome-wide association with independent replication
Who was studied: European-ancestry adults (GEFOS consortium)

1000 Genomes Project

How common each genotype is

How common each genotype is in the 1000 Genomes Project, by region
Region	GGHigher average	AGMiddle	AALower average
All regions2,504 people	8%	35%	56%
Africa661 people	17%	48%	36%
The Americas347 people	7%	32%	62%
East Asia504 people	1%	22%	77%
Europe503 people	8%	37%	55%
South Asia489 people	6%	33%	61%

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	55%32 of 58 copies read
First farmers6500 to 3000 BC	70%517 of 740 copies read
Bronze Age3000 to 1200 BC	74%463 of 627 copies read
Iron Age and Antiquity1200 BC to AD 600	73%600 of 817 copies read
Middle AgesAD 600 to 1500	74%402 of 540 copies read
Today1000 Genomes	74%741 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.

rs3801387

The marker

Gene or region: WNT16
Marker: rs3801387
Location: Chromosome 7 · GRCh37 120,974,765 · GRCh38 121,334,711
Letters studied: A and G, with A 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: WNT16 · rs3801387
Location: Chromosome 7 · GRCh37 120,974,765 · GRCh38 121,334,711
Studied allele: A
Published statistic: Lumbar spine: -0.10 SD per A (Stage 2 estimate), P stage 1 1.4e-16, stage 2 1.5e-36, combined 3.2e-51 (77,508); femoral neck: -0.08 SD per A, combined P 5.0e-40 (83,894); A frequency 0.74 (Table 1); 0.1 SD per copy (Table 1 (LS-BMD, Stage 2))
1000 Genomes Project phase 3, people with 0, 1 and 2 copies: All regions 209 / 884 / 1411 · Africa 110 / 316 / 235 · The Americas 23 / 110 / 214 · East Asia 6 / 110 / 388 · Europe 40 / 185 / 278 · South Asia 30 / 163 / 296

See this card in the sample report

Limits

What it cannot tell you

The studied trait was bone mineral density measured by DXA in adults, and this is one of many markers that influence it.

Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture (Estrada et al., 2012)

The same topic

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