Inferring ancestry and physical characteristics of an unknown individual can contribute to the direction of the investigation and to clarify the event for unknown contributors, cold cases or identification of missing persons and disaster victims. The objective of this study is to develop a custom SNP panel on massively parallel sequencing devices for predicting the biogeographic ancestry and phenotype of an individual. We focused on a two-tier approach to enhance ancestry. Our MPS panel contains two ancestry informative SNP (AISNPs) panels (i.e., Kidd 55 and SWA panel) to differentiate Southwest Asia from Europe and other continental regions. Then we integrated the set of phenotype informative SNPs into a set of AISNPs. The final set of 156 SNPs was evaluated on the following: sensitivity, genotype concordance, mixtures, ancestry assignment, and phenotype prediction. SNP rs6599400 had consistently poor performance and was removed from further analyses. The extreme mixture (1:10) was difficult to interpret for minor contributor. Ancestry assignment and phenotype predictions (for eye, hair and skin) were accurate for samples' population origin. The results show that the developed panel provides high coverage data that can be used for inferring ancestry and predicting eye, hair, and skin color from the intermediate population regions.