SLC24A4 rs4900109: What Your Genotype Means
The rs4900109 variant is a single nucleotide polymorphism located in the SLC24A4 gene region. It is statistically associated with variations in human pigmentation, specifically influencing hair and eye color traits.
What each genotype means
Typical pigmentation profile
This genotype is associated with a higher likelihood of brown hair and brown eye pigmentation. These associations are based on statistical trends observed in large population studies and do not determine individual traits definitively.
This is the most common genotype in many global populations, though frequencies vary significantly by ancestry.
Intermediate pigmentation association
Carrying one copy of the variant is associated with a moderate influence on hair and eye color pigmentation. Research suggests this genotype contributes to the polygenic architecture of human pigmentation, often linked to lighter hair or eye color shades compared to the CC genotype.
This heterozygous genotype is found in approximately 1 in 3 individuals of European ancestry.
Increased lighter pigmentation likelihood
This genotype is statistically linked to an increased likelihood of blond hair and blue or lighter eye pigmentation. As pigmentation is a complex trait influenced by many genes, this variant represents only one factor in your overall genetic profile.
This genotype is most frequently observed in populations of European ancestry and is rare in African and East Asian populations.
Understanding the rs4900109 Variant
The rs4900109 variant is a single nucleotide polymorphism (SNP) situated on chromosome 14 at position 14q32.12. It is located in an intergenic region upstream of the SLC24A4 gene. In genetics, a SNP represents a variation at a single position in the DNA sequence among individuals. While many SNPs have no observable effect on physical traits, some are located in regions that influence how genes are expressed or regulated. The rs4900109 marker is frequently studied alongside other variants in the SLC24A4 locus because it sits within a region known to be involved in the complex genetic architecture of human pigmentation. Researchers use these markers to map how specific DNA sequences correlate with visible physical characteristics across different human populations.
The Role of the SLC24A4 Gene
The SLC24A4 gene encodes a protein known as a sodium/potassium/calcium exchanger. This protein functions as an antiporter, a type of membrane protein that moves ions across cell membranes to maintain cellular balance. Specifically, it is involved in the transport of calcium and potassium ions in exchange for sodium ions. Beyond its role in pigmentation, this gene is essential for proper enamel maturation in teeth; mutations in the coding regions of this gene have been linked to a condition called hypomaturation-type amelogenesis imperfecta. In the context of pigmentation, the gene is thought to influence the development and function of melanocytes, the cells responsible for producing melanin, which determines the color of our skin, hair, and eyes.
Research and Evidence Strength
The association between the SLC24A4 locus and pigmentation is well-documented in scientific literature, particularly regarding hair and eye color. Studies have consistently identified variants in this region as having a statistical link to traits such as blue versus brown eye color and hair color variation. However, the evidence for rs4900109 specifically is considered limited in terms of its individual functional impact. While it is in high linkage disequilibrium with other variants that have stronger, well-established associations with pigmentation, rs4900109 itself is often used as a marker in genome-wide association studies (GWAS). It is important to note that these associations are statistical correlations observed in large cohorts and do not imply a direct, singular cause-and-effect relationship for an individual's physical appearance.
Population Frequency
The distribution of the rs4900109 variant varies significantly across different ancestral groups. Research indicates that the minor allele frequency for this variant is approximately 0.20 in populations of European ancestry. Conversely, the variant is reported to be rare in populations of African and East Asian descent. These differences in frequency are common in human genetics and often reflect historical patterns of migration, natural selection, and genetic drift. Because the variant is much more common in European cohorts, most of the research regarding its association with pigmentation traits has been conducted within these specific populations. Consequently, the applicability of these findings to other global populations remains limited.
Interpreting Your Genetic Information
Information regarding genetic variants like rs4900109 is intended for educational and research purposes only. While it is fascinating to understand the genetic markers associated with physical traits, it is crucial to remember that complex traits like hair and eye color are polygenic, meaning they are influenced by the interaction of many different genes and environmental factors. You cannot use this information to predict your physical appearance with certainty, nor does it provide medical diagnostic value. If you have questions about your genetic results or concerns about your health, you should consult with a qualified healthcare professional or a genetic counselor. They can provide context based on your full medical history and help you understand the limitations of current genetic testing.
How common is this variant?
The minor allele frequency is approximately 0.20 in European populations, while the variant is rare in African and East Asian ancestries.
Frequently asked questions
Can I use rs4900109 to predict my child's eye color?
No, you cannot use this variant to predict eye color. Pigmentation is a complex trait influenced by many genes, and rs4900109 only provides a small, statistical piece of the puzzle.
Is rs4900109 a medical diagnostic marker?
No, rs4900109 is not a medical diagnostic marker. It is a genetic variant associated with normal human variation in pigmentation traits.
Why is this variant more common in Europeans?
Genetic variants often show different frequencies across populations due to historical factors like natural selection, migration, and genetic drift. This specific variant became more prevalent in European populations over time.
Does this variant affect my risk for skin cancer?
While some pigmentation genes are linked to skin sensitivity, there is no evidence that rs4900109 itself is a clinical marker for skin cancer risk. Always consult a dermatologist for skin health concerns.
Sources & further reading
Educational information only, last refreshed 10/26/2026. Not medical advice — these associations describe population statistics, not individual predictions.
Curious what your genotype is for rs4900109?
Upload a raw DNA file from 23andMe, AncestryDNA, MyHeritage, or FamilyTreeDNA and see this variant — plus thousands more — interpreted in your full report.
Get my report — $29Related variants in SLC24A4
Common non-coding variant significantly associated with hair color variation (blonde vs dark) and blue vs brown eye color.
Genomic variant associated with human pigmentation traits, specifically hair and eye color variation.
Intergenic regulatory variant associated with hair and eye color pigmentation variation in European ancestry populations.
Variant near SLC24A4 associated with human hair and eye color pigmentation.
This intergenic variant near the SLC24A4 and KITLG locus is strongly associated with normal variation in human pigmentation, specifically determining blue versus brown eye color and hair color.
Variant in the SLC24A4 region strongly associated with natural blonde hair color and skin pigmentation variation.