Evidence · Replicated

What the research found

In the cited research, the A allele at rs1570669 was associated with lower serum calcium concentrations in the studied cohorts.

GG: Higher average
AG: Middle
AA: Lower average

What the study found

In the study, each copy went with serum calcium about 0.02 mg/dL lower on average.

European-ancestry adults in seventeen discovery cohorts and independent replication cohorts · 60,966 people · Table 1 (Meta-analysis columns); Methods for the unit

Evidence: Genome-wide association with independent replication
Who was studied: European-ancestry adults in many cohorts

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	24%	46%	29%
Africa661 people	38%	49%	14%
The Americas347 people	13%	42%	46%
East Asia504 people	38%	46%	16%
Europe503 people	10%	43%	47%
South Asia489 people	14%	51%	35%

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	65%43 of 66 copies read
First farmers6500 to 3000 BC	74%684 of 923 copies read
Bronze Age3000 to 1200 BC	71%628 of 879 copies read
Iron Age and Antiquity1200 BC to AD 600	70%777 of 1,107 copies read
Middle AgesAD 600 to 1500	65%397 of 612 copies read
Today1000 Genomes	68%686 of 1,006 copies

Neanderthal and Denisovan genomes

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

rs1570669

The marker

Gene or region: CYP24A1
Marker: rs1570669
Location: Chromosome 20 · GRCh37 52,774,427 · GRCh38 54,157,888
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: CYP24A1 · rs1570669
Location: Chromosome 20 · GRCh37 52,774,427 · GRCh38 54,157,888
Studied allele: A
Published statistic: beta -0.018 mg/dL per A (SE 0.003): discovery P 4.0e-8 (N 39,400); replication -0.020 (0.005), P 4.5e-5 (N 21,566); meta-analysis P 9.1e-12 (N 60,966), I2 0 (Table 1). A also with higher PTH (beta 0.035, P 0.0005) and lower femoral neck BMD (P 0.04) (Table 2). Unit: untransformed serum calcium in mg/dL (Methods) (Table 1 (Meta-analysis columns); Methods for the unit)
1000 Genomes Project phase 3, people with 0, 1 and 2 copies: All regions 606 / 1161 / 737 · Africa 249 / 321 / 91 · The Americas 44 / 145 / 158 · East Asia 191 / 230 / 83 · Europe 52 / 216 / 235 · South Asia 70 / 249 / 170

See this card in the sample report

Limits

What it cannot tell you

Serum calcium is tightly held, and the per-copy difference is very small. CYP24A1 breaks down active vitamin D, which this card does not measure.

Meta-analysis of genome-wide association studies identifies six new loci for serum calcium concentrations (O'Seaghdha et al., 2013)

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