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Introduction: Human eye colour as a physical trait is based on the developmental biology and genetic determinants of the structure known as the iris, which is part of the uveal tract of the eye. Prediction of human visible characteristics (EVCs) by genotyping informative SNPs in DNA as biological witness opens up a new avenue in the forensic genetic. Variation of iris color rely on the amounts of eumelanine and pheomelanin. The aim of this research was to determine and evaluate the frequency and the association of rs12913832 with prediction of human eye color in 53 volunteer of Iranian population samples. Methods: A selection of human body blood samples were collected from donors with informed consent in Clinic Ophthalmology of Baqiyatallah hospital. DNA was extracted from the samples using RGDE procedure. PCR primers for rs12913832 were designed to give amplicon sizes up to 189 bp and Single base extensions (SBE) were done by applying the SNaPshot Multiplex kit in 6 ;mul reaction volumes. The results were analyzed with the SPSS 22.0 software package. Results: The frequency of eye color were achieved for brown 34%, blue 17% and intermediate colors 49%, respectively. The genotype frequencies of T/T, C/T and C/C in our population were 4.26 %, 8.35 % and 7.37%, respectively. The statistical analysis revealed the two genotypes including T/T and C/C had a significant associate with dark brown eyes and bright blue eyes, respectively. The sensitivity and specificity of our method were determined 100% and 56.25%,respectively. Conclusion: Our results demonstrated that rs12913832 C>T polymorphism is associated with blue iris color in Iranian population. However, assessment SNP markers by using SNaPshot is a key tool for tracing unknown persons to get primarily information about genotypic and phenotypic characteristics.