TNF-α promoter single nucleotide polymorphisms are markers of human ancestry

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Abstract
We present a map of single nucleotide polymorphisms (SNPs) in the human tumor necrosis factor (TNF)-α promoter based upon exploratory sequencing of 333 human TNF-α gene promoters from individuals of distinct ancestral backgrounds. We detect 10 TNF-α promoter SNPs that occur with distinct frequencies in populations of different ancestry. Consistent with these findings, we show that two TNF-α SNPs, the −243 SNP and the −856 SNP, are the first SNP markers of a sub-Saharan African-derived extended haplotype and an Amerindian HLA haplotype, respectively. Comparisons of TNF-α promoter SNP allele frequencies can thus help elucidate variation of HLA haplotypes and their distribution among existing ethnic groups and shed light into the history of human populations.