Periodontitis is the major causation of tooth loss in the elderly population. Multiple risk factors include oral microorganisms, smoking, metabolic syndrome, and genetic factors influence periodontitis development. In this study, we conducted a replication study of using previous Korean GWAS results by examining an independent population. The study population was recruited from Mir Dental Clinic, Daegu, Korea. In total, 93 samples were evaluated from July 2016 to January 2017. The sample groups include relatively older patients (>60 years) with no periodontitis (n = 31) and relatively younger patients (range 40~60 years) with severe periodontitis (n = 62). A total of seven markers which were previously reported to be associated with periodontitis were genotyped. Among the seven SNPs, rs16846206 and rs2392510 showed a significant association by logistic regression analysis and Chi square test, respectively. The former SNP showed significant association with severe periodontitis, whereas this study also showed same tendency in which individuals with the minor allele are significantly more frequent in cases than those in controls. The SNP is located on a coding gene (SLC9C2), where the alanine residue 505 is replaced by glycine (Ala505Gly). The later SNP was significant when differed between case and control groups, but there was no significance by logistic regression analysis when controlled for age and sex as covariant. Although the study population size examined in the current study was relatively smaller compared to previous studies, our results implicated that at least the two SNPs (rs16846206 and rs2392510) might be important candidates for the further genetic study.