DNA Traits · Appearance
Eye pigmentation (SLC24A4)
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 T allele at rs12896399 was associated with lighter eye pigmentation.
- GG
- Darker range
- GT
- Middle
- TT
- Lighter range
Modest effect
What the study found
In the study, each copy went with eye colour score from blue to brown on a seven step survey scale about 0.34 points lower on average.
23andMe research participants of northern European ancestry · 4,402 people · Table 4 (Eye color, rs12896399); sample size Table 1
- Evidence
- Genome-wide association with independent replication
- Who was studied
- European ancestry (Icelandic and Dutch participants; 23andMe research participants of northern European ancestry)
1000 Genomes Project
How common each genotype is
| Region | GGDarker range | GTMiddle | TTLighter range |
|---|---|---|---|
| All regions2,504 people | 58% | 33% | 10% |
| Africa661 people | 96% | 4% | Not seen |
| The Americas347 people | 56% | 38% | 6% |
| East Asia504 people | 44% | 42% | 13% |
| Europe503 people | 34% | 46% | 20% |
| South Asia489 people | 45% | 44% | 11% |
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
Europe
| Before farmingbefore 6500 BC | 22%18 of 83 copies read |
|---|---|
| First farmers6500 to 3000 BC | 32%235 of 728 copies read |
| Bronze Age3000 to 1200 BC | 30%207 of 680 copies read |
| Iron Age and Antiquity1200 BC to AD 600 | 42%515 of 1,218 copies read |
| Middle AgesAD 600 to 1500 | 44%586 of 1,337 copies read |
| Today1000 Genomes | 43%433 of 1,006 copies |
Neanderthal and Denisovan genomes
- Altai Neanderthal
- No copies
- Vindija Neanderthal
- No copies
- Chagyrskaya Neanderthal
- No copies
- Denisovan
- No copies
Neanderthals and Denisovans carried the other letter, so this letter is younger than our split with them.
rs12896399
The marker
- Gene or region
- SLC24A4
- Marker
- rs12896399
- Location
- Chromosome 14 · GRCh37 92,773,663 · GRCh38 92,307,319
- Letters studied
- G 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
- SLC24A4 · rs12896399
- Location
- Chromosome 14 · GRCh37 92,773,663 · GRCh38 92,307,319
- Studied allele
- T
- Published statistic
- beta -0.343 per T allele on the zero to six blue to brown scale, score 15.95 (P about 1.1e-16), n 4,402, within Eriksson's replication of known eye colour loci (Table 4); Sulem 2007: OR 2.06 per T for blue versus green eyes, P 4e-38, and OR 2.56 per T for blond versus brown hair, P 1e-48 (GWAS Catalog GCST000117 and GCST000118; the paper is not open access and its tables were not read); Simcoe 2021 Table 1 region 38: the neighbouring lead rs17184180, which has r2 0.98 with this marker in 1000 Genomes Europeans, gives beta 0.271 per its T toward dark brown, P 1.34e-284, n 157,483; Hysi 2018: hair colour beta 0.181 per allele, P 1e-100 (Table 4 (Eye color, rs12896399); sample size Table 1)
- 1000 Genomes Project phase 3, people with 0, 1 and 2 copies
- All regions 1443 / 816 / 245 · Africa 633 / 28 / 0 · The Americas 194 / 131 / 22 · East Asia 222 / 214 / 68 · Europe 172 / 229 / 102 · South Asia 222 / 214 / 53
Limits
What it cannot tell you
Almost always inherited together with the SLC24A4 hair-lightness marker, so those cards are not independent evidence.
Web-based, participant-driven studies yield novel genetic associations for common traits (Eriksson et al., 2010)The same topic
More in Appearance
- Eye pigmentation
- Red hair association
- Blond hair association
- Hair shape
- Hair thickness association
- Skin pigmentation
- Freckling association
- Hair greying association
- Eyebrow thickness association
- Beard density association
- Unibrow association
- Nose bridge breadth association
- Nose wing breadth association
- Nose protrusion association
- Nose tip angle association
- Chin protrusion association
- Earlobe attachment association
- Earlobe size association
- Ear ridge folding association
- Male pattern hair loss
- Male pattern hair loss, HDAC9 marker
- Male pattern hair loss, EBF1 marker
- Male pattern hair loss, WNT10A marker
- Hair lightness, SLC24A4 marker
- Blond hair, TPCN2 marker
- Hair lightness, SLC45A2 marker
- Red hair, ASIP region marker
- Hair lightness, HERC2 marker
- Hair colour, IRF4 marker
- Hair shape, WNT10A marker
- Hair shape, PADI3 marker
- Hair shape, HOXC13 marker
- Hair shape, GATA3 region marker
- Hair shape, FRAS1 marker
- Hair shape, LCE3E marker
- Straight hair, EDAR marker
- Eyebrow thickness, FOXD1 region marker
- Eyebrow thickness, FOXL2 marker
- Shovel-shaped incisors
- Finger length ratio (SMOC1 marker)
- Finger length ratio (LDAH marker)
- Finger length ratio (SALL1 marker)
- Finger length ratio (OLA1 marker)
- Nose root position
- Nose wing breadth (PAX1 marker)
- Earlobe attachment (PAX9 marker)
- Earlobe attachment (KIAA1217 marker)
- Earlobe attachment (MRPS22 marker)
- Fingerprint whorls (ADAMTS9 marker)
- Fingerprint whorls (EVI1 marker)
- Fingerprint whorls (SALL3 marker)
- Green or hazel eyes
- Eye pigmentation (TYR)
- Freckling (TYR)
- Skin pigmentation (OCA2 H615R)
- Freckling (PPARGC1B)
- Freckling (HSPA12A)
- Freckling (BNC2)
- Freckling (EMX2)
- Freckling (EIF6, ASIP region)
- Skin lightness (OCA2 A481T)
- Eye pigmentation (TSPAN10)
- Eye pigmentation (TYRP1)
- Eye pigmentation (SIK1)
- Eye pigmentation (OCA2 exon ten)
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