SLC45A2 rs11146244: Hair and Eye Pigmentation Variant
The rs11146244 single nucleotide polymorphism is a downstream non-coding variant located near the SLC45A2 gene. Research shows it functions as a regulatory element associated with modulating SLC45A2 expression levels, which in turn influences normal human variation in eye and hair pigmentation. Evidence supporting its contribution to lighter iris and hair shades is considered limited compared to major coding variants in the same locus.
What each genotype means
Associated with darker pigmentation
This genotype is associated with higher levels of SLC45A2 expression, which typically correlates with darker hair and iris pigmentation in many populations. Because this is a regulatory variant, its influence on physical traits is statistical rather than deterministic, and individual results may vary significantly based on other genetic and environmental factors.
This genotype is the major allele in many non-European populations and is common globally.
Intermediate pigmentation association
Carrying one copy of the G allele may result in a phenotype intermediate between those with the CC and GG genotypes regarding hair and iris shade. Research indicates this variant acts as a downstream regulator of SLC45A2, and this heterozygous state reflects a balanced contribution to the expression levels that influence melanin production.
This genotype is found at moderate frequencies in European populations where the G allele is more prevalent.
Associated with lighter pigmentation
This genotype is statistically associated with lower SLC45A2 expression levels, which often correlates with lighter hair and iris pigmentation in European populations. As a regulatory SNP, it contributes to the natural variation in human pigmentation, though it does not dictate specific physical traits on its own.
Carried by roughly 1 in 6 people of European ancestry; it is significantly less common in East Asian and African populations.
Genomic Location and Regulatory Role
The single nucleotide polymorphism rs11146244 is located on human chromosome 5 downstream of the SLC45A2 gene. Unlike missense mutations that directly alter the amino acid sequence of a protein, rs11146244 resides in a non-coding region. Functional and expression quantitative trait locus studies suggest that this variant falls within a regulatory sequence capable of modifying transcript levels of SLC45A2. By subtly influencing how much mRNA is transcribed, downstream variants like rs11146244 can fine-tune cellular pathways without producing a defective or altered protein product. Because non-coding regions often act in concert with complex enhancer-promoter loops, mapping the exact functional mechanisms of such variants remains an active area of study in human genetics.
SLC45A2 and Melanin Biosynthesis
The SLC45A2 gene, historically known as MATP (Membrane-Associated Transporter Protein), encodes a multi-pass transmembrane transporter located in melanocytes. Melanocytes are specialized cells responsible for producing melanin, the pigment that determines the shade of human skin, hair, and irises. Melanosomes require a carefully regulated internal pH and ionic environment to facilitate the enzymatic activity of tyrosinase, the rate-limiting enzyme in melanin production. Pathogenic disruptions of SLC45A2 lead to oculocutaneous albinism type 4 (OCA4), illustrating the gene's essential role in normal pigmentation. Subtle regulatory modifications that alter SLC45A2 expression modulate the balance and density of melanin synthesis, leading to non-pathological shifts along the continuous spectrum of human visible traits.
Associated Traits and Strength of Evidence
Genome-wide association studies and candidate gene screens have linked rs11146244 to subtle shifts in iris lightness and lighter shades of hair. However, the overall strength of scientific evidence linking rs11146244 directly to pigmentation phenotypes is categorized as limited. While SLC45A2 as a whole is a primary determinant of pigmentation diversity, much of the measurable phenotypic effect in European and global populations is driven by well-characterized coding variants, such as rs16891982 (p.Phe374Leu). Variant rs11146244 frequently tags regulatory haplotypes or acts as a secondary modifier. Because its isolated effect size is modest, it does not function as a standalone determinant of physical appearance, but rather as one of many minor polygenic contributors.
Interpreting Your Genetic Results Responsibly
Discovering your rs11146244 genotype provides an interesting glimpse into the polygenic architecture of human pigmentation, but it has important limitations. Human eye and hair colors are complex multifactorial traits governed by dozens of interconnected loci, including HERC2, OCA2, TYR, and MC1R, alongside SLC45A2. Carrying an allele associated with lighter hair or eyes does not guarantee any specific visible shade, nor does it override other major ancestral alleles. Crucially, rs11146244 is a benign trait modifier and not a clinical diagnosis. It provides no diagnostic value for inherited pigmentation disorders like albinism, nor does it serve as a direct clinical guide for dermatological care.
How common is this variant?
The minor allele at rs11146244 exhibits a frequency of approximately 0.18 (18%) in European populations, but it is exceedingly rare or virtually absent in East Asian and African ancestral groups.
Frequently asked questions
Does my rs11146244 genotype determine my exact eye color?
No, rs11146244 alone cannot determine your eye color. Human eye pigmentation is polygenic, meaning it is shaped by the combined activity of dozens of genetic variants across multiple genes, most notably HERC2 and OCA2. At most, rs11146244 acts as a minor modifier with limited statistical effect.
Is rs11146244 linked to albinism or medical skin conditions?
No, rs11146244 is a non-coding regulatory variant associated only with common physiological variation in physical traits. While rare, loss-of-function mutations in the SLC45A2 gene cause oculocutaneous albinism type 4 (OCA4), rs11146244 does not cause albinism or any known clinical disorder.
Why is this variant more common in European populations than in other ancestries?
Many variants within pigmentation-related genes like SLC45A2 underwent regional selective sweeps or genetic drift as human populations diversified across different latitudes and UV environments. Consequently, alleles associated with lighter shades of hair, eyes, and skin frequently reach moderate frequencies in northern and western European groups while remaining rare in equatorial and East Asian populations.
Can commercial DNA testing use rs11146244 for forensic or physical prediction?
Forensic phenotyping panels generally prioritize major functional variants with strong, reproducible effect sizes, such as rs16891982 in SLC45A2 or rs12913832 in HERC2. Because the scientific evidence linking rs11146244 to observable appearance is classified as limited, it rarely serves as a primary marker in predictive forensic models.
Sources & further reading
Educational information only, last refreshed 9/6/2026. Not medical advice — these associations describe population statistics, not individual predictions.
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This synonymous variant is in high linkage disequilibrium with functional alleles that influence human skin, hair, and eye pigmentation.
This missense variant (p.Phe374Leu) is a major determinant of human skin, hair, and eye pigmentation, showing strong evidence of selection in European populations.
Synonymous marker in the SLC45A2 locus associated with skin reflectance, tanning response, and freckling phenotypes.
This missense variant (p.Phe374Leu) is a key ancestry-informative marker and a classic signature of recent positive selection, strongly associated with skin pigmentation and melanoma risk.
This variant (p.Phe374Leu) is strongly associated with lighter skin, hair, and eye pigmentation, as well as an increased sensitivity to UV-induced skin damage.
The p.Phe374Leu variant in SLC45A2 is a major determinant of human pigmentation variation, influencing skin, hair, and eye color across global populations.