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Genetic data on North Central Asian populations are under-represented in the literature, especially autosomal markers. In the present study we use 812 single nucleotide polymorphisms that are distributed across all the human autosomes and that have been extensively studied at Yale to examine the affinities of two recently collected, samples of populations: rural and cosmopolitan Mongolians from Ulaanbaatar and nomadic, Turkic-speaking Tsaatan from Mongolia near the Siberian border. We compare these two populations to one another and to a global set of populations and discuss their relationships to New World populations. Specifically, we analyze data on 521 autosomal loci (single SNPs and multi-SNP haplotypes) studied on 57 populations representing all the major geographical regions of the world. We conclude that the North Central Asian populations we study are genetically distinct from all other populations in our study and may be close to the ancestral lineage leading to the New World populations.