“GWAS in Almost 195,000 Individuals Identifies 50 Previously Unidentified Genetic Loci for Eye Color”, Mark Simcoe, Ana Valdes, Fan Liu, Nicholas A. Furlotte, David M. Evans Gibran Hemani Susan M. Ring George Davey Smith David L. Duffy, Gu Zhu, Scott D. Gordon, Sarah E. Medland, Dragana Vuckovic, Giorgia Girotto Cinzia Sala, Eulalia Catamo, Maria Pina Concas, Marco Brumat, Paolo Gasparini Daniela Toniolo, Massimiliano Cocca, Antonietta Robino, Seyhan Yazar, Alex Hewitt, Wenting Wu, Peter Kraft, Christopher J. Hammond Yuan Shi, Yan Chen, Changqing Zeng, Caroline C. W. Klaver, Andre G. Uitterlinden M. Arfan Ikram, Merel A. Hamer, Cornelia M. van Duijn Tamar Nijsten, Jiali Han, David A. Mackey, Nicholas G. Martin, Ching-Yu Cheng, the 23andMe Research Team, the International Visible Trait Genetics Consortium, David A. Hinds, Timothy D. Spector, Manfred Kayser, Pirro G. Hysi2021-03-10 (neural net, heritability; similar)⁠:

Human eye color is highly heritable, but its genetic architecture is not yet fully understood.

We report the results of the largest genome-wide association study for eye color to date, involving up to 192,986 European participants from 10 populations. We identify 124 independent associations arising from 61 discrete genomic regions, including 50 previously unidentified. We find evidence for genes involved in melanin pigmentation, but we also find associations with genes involved in iris morphology and structure. Further analyses in 1636 Asian participants from two populations suggest that iris pigmentation variation in Asians is genetically similar to Europeans, albeit with smaller effect sizes. Our findings collectively explain 53.2% (95% confidence interval, 45.4 to 61.0%) of eye color variation using common single-nucleotide polymorphisms.

Overall, our study outcomes demonstrate that the genetic complexity of human eye color considerably exceeds previous knowledge and expectations, highlighting eye color as a genetically highly complex human trait.

…In Europeans, the 112 autosomal SNPs identified through conditional analysis (all autosomal SNPs shown in table S1) explained 99.96% (SE = 6.5%, p = 4.8 × 10⁻²⁷⁹) of the liability scale for blue eyes (against brown eyes) and 38.5% (SE = 5.7%, p = 2.2 × 10⁻¹³⁰) for intermediate eyes in the TwinsUK cohort, which was one of the VisiGen cohorts used for replication. Using the same linear scale as the GWAS analysis, these autosomal SNPs explained 53.2% (SE = 4.0%, p = 1.2 × 10⁻³²²) of the total phenotypic variation in eye color in TwinsUK.

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