DNA Traits · Appearance

Freckling (HSPA12A)

Whether people report having freckles, the small tan spots the sun brings out.

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Evidence · Replicated

What the research found

In the cited research, the T allele at rs12259842 was associated with reporting freckles more often in the studied East Asian cohorts.

CC: Less often
CT: Middle
TT: More often

Modest effect

Evidence: Genome-wide association in Japanese women, replicated in an independent Chinese study
Who was studied: East Asian ancestry (Chinese men and women; Japanese women in the earlier study)

1000 Genomes Project

How common each genotype is

How common each genotype is in the 1000 Genomes Project, by region
Region	CCLess often	CTMiddle	TTMore often
All regions2,504 people	63%	31%	6%
Africa661 people	87%	12%	<1%
The Americas347 people	60%	35%	5%
East Asia504 people	63%	32%	5%
Europe503 people	60%	36%	4%
South Asia489 people	38%	47%	15%

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.

rs12259842

The marker

Gene or region: HSPA12A
Marker: rs12259842
Location: Chromosome 10 · GRCh37 118,455,243 · GRCh38 116,695,732
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: HSPA12A · rs12259842
Location: Chromosome 10 · GRCh37 118,455,243 · GRCh38 116,695,732
Studied allele: T
Published statistic: OR 1.46 (1.33 to 1.61) per the C allele of the proxy rs12245621 for reported freckles, P 1.64e-14 in the discovery set of 6,579, with OR 1.33, P 4.80e-3 in the validation set of 1,672 (Wang 2022 Supplementary Tables 2 and 3); the proxy has r2 0.907 with rs12259842 in 1000 Genomes East Asians and its C travels with our T. Endo 2018 Table 1 prints OR 1.23 (1.16 to 1.31) per T for reported freckles in Japanese women, meta-analysis P 7.1e-11 with P 3.0e-7 and 7.8e-5 in its two sample sets (Supplementary Table 3 (Freckles, rs12245621) and Supplementary Table 2 (discovery set size), in the supplementary PDF DataSheet1)
1000 Genomes Project phase 3, people with 0, 1 and 2 copies: All regions 1584 / 782 / 138 · Africa 577 / 82 / 2 · The Americas 207 / 123 / 17 · East Asia 316 / 163 / 25 · Europe 300 / 182 / 21 · South Asia 184 / 232 / 73

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Limits

What it cannot tell you

Studied in East Asian ancestry only, and both studies recorded only whether people reported freckles, never how many.

Novel genetic associations with five aesthetic facial traits: A genome-wide association study in the Chinese population (Wang et al., 2022)

The same topic

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