Evidence · Replicated

What the research found

In the cited research, the G allele at rs12785878 was associated with lower circulating 25-hydroxyvitamin D concentrations in the studied cohorts.

TT: Higher average
GT: Middle
GG: Lower average

Slight effect

What the study found

In the study, the average vitamin D in the blood, by genotype:

TTNo copy: 59.6 nmol/L
GTOne copy: 56.3 nmol/L
GGTwo copies: 55.7 nmol/L

1958 British Birth Cohort participants · 6,552 people · Table 2 (1958 British Birth Cohort column, DHCR7 rows; footnote: rs12785878 in that cohort)

Evidence: Genome-wide association with independent replication
Who was studied: European-ancestry discovery and replication cohorts

1000 Genomes Project

How common each genotype is

How common each genotype is in the 1000 Genomes Project, by region
Region	TTHigher average	GTMiddle	GGLower average
All regions2,504 people	17%	36%	46%
Africa661 people	3%	28%	69%
The Americas347 people	22%	46%	32%
East Asia504 people	14%	49%	38%
Europe503 people	50%	40%	10%
South Asia489 people	3%	23%	73%

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%52 of 94 copies read
First farmers6500 to 3000 BC	54%466 of 871 copies read
Bronze Age3000 to 1200 BC	55%439 of 796 copies read
Iron Age and Antiquity1200 BC to AD 600	44%567 of 1,281 copies read
Middle AgesAD 600 to 1500	39%455 of 1,165 copies read
Today1000 Genomes	30%301 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. Ancient genomes from the Allen Ancient DNA Resource (AADR v66): 15,136 people.

rs12785878

The marker

Gene or region: DHCR7 / NADSYN1
Marker: rs12785878
Location: Chromosome 11 · GRCh37 71,167,449 · GRCh38 71,456,403
Letters studied: G and T, with G 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: DHCR7 / NADSYN1 · rs12785878
Location: Chromosome 11 · GRCh37 71,167,449 · GRCh38 71,456,403
Studied allele: G
Published statistic: 1958 Birth Cohort means (SE) 59.6 (0.31), 56.3 (0.30), 55.7 (0.32) nmol/L for major homozygotes, heterozygotes, minor homozygotes (rs12785878; Table 2). Overall P 2.12e-27 (discovery 1.27e-12, replication 2.39e-16), MAF 0.23 (Table 1). Jiang 2018: T/G, frequency 0.75, beta 0.036 on ln 25(OH)D per T, P 3.80e-62 (Table 1) (Table 2 (1958 British Birth Cohort column, DHCR7 rows; footnote: rs12785878 in that cohort))
1000 Genomes Project phase 3, people with 0, 1 and 2 copies: All regions 433 / 907 / 1164 · Africa 20 / 185 / 456 · The Americas 76 / 160 / 111 · East Asia 69 / 245 / 190 · Europe 251 / 203 / 49 · South Asia 17 / 114 / 358

See this card in the sample report

Limits

What it cannot tell you

DHCR7 acts in the skin's vitamin D pathway, but the study measured only the blood level. In the cohort shown, one copy and two copies averaged almost the same.

Common genetic determinants of vitamin D insufficiency: a genome-wide association study (Wang et al., 2010)

The same topic

More in Nutrition & metabolism

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