Human facial morphology is one of the important visible biological characteristics. Understanding the genetic basis underlying facial shape traits has important implications in population genetics, developmental biology, and forensic science. This study extracted 136 Euclidean distance phenotypes from 17 facial features of high-resolution 3D facial images in 1177 Chinese Han adult males. Based on 3× low-depth sequencing data, linear regression was used to analyze the correlation between 125 reported SNPs significantly associated with facial morphology and 136 facial phenotypes. As a result, a total of twelve SNPs from ten genes demonstrated significant association with one or more facial shape traits after adjusting for multiple testing (significance threshold < 1.35 × 10 ) together explaining up to 3.89% of age-, and BMI-adjusted facial phenotype variance. These included rs17479393, rs974448, rs2977562, rs9995821, rs2045323, rs6555969, rs1852985, rs11782517, rs10504499, rs2224309, rs7161418 and rs2206437.These results revealed the genetics basis of facial morphology of Han Chinese population, and provided reference data for DNA-based face prediction.
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