We conducted a two-step case-control study to investigate the association between mtDNA variants and metabolic syndrome (MS) in Chinese. We initially screened 79 mitochondrial single nucleotide polymorphisms (mtSNPs) in 141 cases and 506 controls, and five mtSNPs had a p<0.05. We replicated results for the most significant mtSNP 10398A>G in additional 396 case and 424 controls (p=0.047, OR=1.26). The G allele frequency in the screening and follow up data was 66% and 55.2% in the cases, and 52.3% and 50.2% in the controls, respectively. Our results suggest the G allele of 10398A>G increases a risk for MS.
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