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Other genes implicated in eye color variation are SLC24A4 and TYR. A specific mutation within the HERC2 gene, a gene that regulates OCA2 expression, is partly responsible for blue eyes. The polymorphisms may be in an OCA2 regulatory sequence, where they may influence the expression of the gene product, which in turn affects pigmentation.

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(The name of the gene is derived from the disorder it causes, oculocutaneous albinism type II.) Different SNPs within OCA2 are strongly associated with blue and green eyes as well as variations in freckling, mole counts, hair and skin tone. The gene OCA2 (OMIM: 203200), when in a variant form, causes the pink eye color and hypopigmentation common in human albinism. There is evidence that as many as 16 different genes could be responsible for eye color in humans however, the main two genes associated with eye color variation are OCA2 and HERC2, and both are localized in Chromosome 15. Through the analysis of ancient DNA, a 2020 study published in Experimental Dermatology suggested that the common gene for blue eye color likely originated in the Near East and arrived in Europe around 42,000 years ago, after the exodus out of Africa. Recent advances in ancient DNA technology have revealed some of the history of eye color in Europe. People of European descent show the greatest variety in eye color of any population worldwide. A study in Rotterdam (2009) found that it was possible to predict eye color with more than 90% accuracy for brown and blue using just six SNPs. The total number of genes that contribute to eye color is unknown, but there are a few likely candidates.

These genes are sought by studying small changes in the genes themselves and in neighboring genes, called single-nucleotide polymorphisms or SNPs. Genetic determinationĮye color is an inherited trait determined by multiple genes. However, OCA2 gene polymorphism, close to proximal 5' regulatory region, explains most human eye-color variation. The genetics of eye color are so complex that almost any parent-child combination of eye colors can occur. The earlier belief that blue eye color is a simple recessive trait has been shown to be incorrect. Some of the eye-color genes include OCA2 and HERC2. As of 2010, as many as 16 genes have been associated with eye color inheritance. The genetics and inheritance of eye color in humans is complicated. Humans and other animals have many phenotypic variations in eye color. The brightly colored eyes of many bird species result from the presence of other pigments, such as pteridines, purines, and carotenoids. This is an example of structural color, which depends on the lighting conditions, especially for lighter-colored eyes. Neither blue nor green pigments are present in the human iris or vitreous humour.

The appearance of blue, green, and hazel eyes results from the Tyndall scattering of light in the stroma, a phenomenon similar to Rayleigh scattering which accounts for the blue sky. In humans, the pigmentation of the iris varies from light brown to black, depending on the concentration of melanin in the iris pigment epithelium (located on the back of the iris), the melanin content within the iris stroma (located at the front of the iris), and the cellular density of the stroma. The irises of human eyes exhibit a wide spectrum of coloursĮye color is a polygenic phenotypic trait determined by two factors: the pigmentation of the eye's iris and the frequency-dependence of the scattering of light by the turbid medium in the stroma of the iris. For the shade of purple, see Iris (color).