Evidence · Replicated

What the research found

In the cited research, the T allele at rs35563099 was associated with reporting freckles less often in the studied East Asian cohorts.

CC: More often
CT: Middle
TT: Less often

Modest effect

Evidence: Genome-wide association with independent replication
Who was studied: East Asian ancestry (Chinese men and women; Japanese women)

1000 Genomes Project

How common each genotype is

How common each genotype is in the 1000 Genomes Project, by region
Region	CCMore often	CTMiddle	TTLess often
All regions2,504 people	72%	25%	3%
Africa661 people	67%	28%	5%
The Americas347 people	81%	18%	<1%
East Asia504 people	81%	18%	<1%
Europe503 people	71%	27%	2%
South Asia489 people	65%	30%	4%

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	27%11 of 41 copies read
First farmers6500 to 3000 BC	19%128 of 673 copies read
Bronze Age3000 to 1200 BC	22%127 of 574 copies read
Iron Age and Antiquity1200 BC to AD 600	17%145 of 830 copies read
Middle AgesAD 600 to 1500	11%47 of 409 copies read
Today1000 Genomes	15%154 of 1,006 copies

Neanderthal and Denisovan genomes

Altai Neanderthal: Not read
Vindija Neanderthal: Not read
Chagyrskaya Neanderthal: No copies
Denisovan: Not read

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.

rs35563099

The marker

Gene or region: EMX2 / RAB11FIP2 region
Marker: rs35563099
Location: Chromosome 10 · GRCh37 119,572,403 · GRCh38 117,812,892
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: EMX2 / RAB11FIP2 region · rs35563099
Location: Chromosome 10 · GRCh37 119,572,403 · GRCh38 117,812,892
Studied allele: T
Published statistic: OR 0.60 (0.51 to 0.71) per T allele for freckles, P 3.51e-9, validation OR 0.58, P 1.07e-3, n 8,251 (Wang 2022 Supplementary Tables 2 and 3); Endo 2018 Table 1: OR 0.78 (0.70 to 0.86) per T for age spots and freckles shared, P 1.2e-6 as a secondary signal, while the region's own freckles lead rs10444039, which has r2 0.99 with this marker in 1000 Genomes East Asians, gives OR 0.60 (0.54 to 0.67) per A, P 5.6e-21 (Supplementary Table 3 (Freckles, rs35563099) 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 1810 / 623 / 71 · Africa 443 / 184 / 34 · The Americas 282 / 63 / 2 · East Asia 407 / 92 / 5 · Europe 358 / 136 / 9 · South Asia 320 / 148 / 21

See this card in the sample report

Limits

What it cannot tell you

The same marker as the EMX2 tanning card; the freckles result comes from East Asian studies only, and they recorded only whether people reported freckles.

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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