DNA Traits · Appearance

Eye pigmentation (TSPAN10)

How much pigment the iris holds, from blue towards brown.

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Evidence · Replicated

What the research found

In the cited research, the G allele at rs6420484 was associated with lighter eye pigmentation.

AA: Darker range
AG: Middle
GG: Lighter range

Slight effect

What the study found

In the study, each copy went with eye colour score from blue to dark brown on a seven step self-rated scale about 0.16 points lower on average.

23andMe research participants of European ancestry · 157,483 people · Table 1, region 45 (rs6420484: reference allele G, frequency 0.645, beta -0.161, SE 0.0080, P 7.53e-90)

Evidence: Genome-wide association at a previously reported locus
Who was studied: European ancestry (23andMe research participants; the Rotterdam Study for the earlier report)

1000 Genomes Project

How common each genotype is

How common each genotype is in the 1000 Genomes Project, by region
Region	AADarker range	AGMiddle	GGLighter range
All regions2,504 people	5%	21%	74%
Africa661 people	<1%	9%	90%
The Americas347 people	6%	32%	62%
East Asia504 people	Not seen	<1%	>99%
Europe503 people	14%	43%	43%
South Asia489 people	5%	30%	65%

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.

rs6420484

The marker

Gene or region: TSPAN10 (reported earlier as NPLOC4)
Marker: rs6420484
Location: Chromosome 17 · GRCh37 79,612,397 · GRCh38 81,645,371
Letters studied: A and G, 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: TSPAN10 (reported earlier as NPLOC4) · rs6420484
Location: Chromosome 17 · GRCh37 79,612,397 · GRCh38 81,645,371
Studied allele: G
Published statistic: beta -0.161 (SE 0.0080) per G allele on the zero to six eye colour scale, P 7.53e-90, n 157,483 (Simcoe 2021 Table 1, region 45); Simcoe's Results name it one of four previously reported loci confirmed here, reported earlier as NPLOC4; of the 48 lead SNPs taken to the independent VisiGen replication (n 35,501), 47 kept the same direction and 27 passed a Bonferroni threshold, but the per-SNP replication figures are in table ST4, which the publisher blocks (Table 1, region 45 (rs6420484: reference allele G, frequency 0.645, beta -0.161, SE 0.0080, P 7.53e-90))
1000 Genomes Project phase 3, people with 0, 1 and 2 copies: All regions 120 / 538 / 1846 · Africa 4 / 62 / 595 · The Americas 21 / 112 / 214 · East Asia 0 / 3 / 501 · Europe 72 / 215 / 216 · South Asia 23 / 146 / 320

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Limits

What it cannot tell you

Studied in European ancestry only; outside Europe the studied letter is almost the only one present.

Genome-wide association study in almost 195,000 individuals identifies 50 previously unidentified genetic loci for eye color (Simcoe et al., 2021)

The same topic

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