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We recently performed an Epigenome-Wide Association Studies (EWAS) study in Behcet\u2019s disease (BD) and identified various cytosine\u2013phosphate\u2013guanine (CpG) loci that were aberrantly methylated. In the current study, we wanted to investigate whether these sites contained genetic polymorphisms and whether the frequency of these polymorphisms was altered in BD.<jats:italic>Methods<\/jats:italic>. A two-stage study was performed. The first stage involved 358 BD patients and 704 healthy controls to investigate genetic variants of 10 CpG-SNPs (rs10454134, rs176249, rs3808620, rs10176517, rs11247118, rs78016579, rs9461624, rs10492166, rs34929465, and rs6507921) using an iPLEX Gold genotyping assay and a Sequenom MassARRAY. In the second stage, an additional 172 independent BD patients and 330 healthy individuals are to confirm trends found in the first stage.<jats:italic>Results<\/jats:italic>. A higher frequency of both the rs10454134 AG genotypes (p = 0.008, OR = 1.413, 95% CI = 1.094-1.826) and a lower GG genotype frequency (p = 0.003, OR = 0.630, 95% CI = 0.465-0.854) were found in BD patients compared to the controls in the first stage. However, after correcting for multiple comparisons, all associations identified in the first stage lost statistical significance. The frequencies of the other CpG-SNPs investigated were not different between BD patients and controls. The second stage was designed using an additional cohort to confirm the association with CpG-SNP, rs10454134. The data failed to confirm the association between this CpG-SNP and BD.<jats:italic>Conclusions<\/jats:italic>. This study did not show an association between BD and CpG-SNPs in gene sites that were earlier shown to be aberrantly methylated.<\/jats:p>","DOI":"10.1155\/2019\/3489305","type":"journal-article","created":{"date-parts":[[2019,5,16]],"date-time":"2019-05-16T23:31:19Z","timestamp":1558049479000},"page":"1-7","source":"Crossref","is-referenced-by-count":2,"title":["Different Methylation of CpG-SNPs in Behcet\u2019s Disease"],"prefix":"10.1155","volume":"2019","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7761-9819","authenticated-orcid":true,"given":"Yang","family":"Huang","sequence":"first","affiliation":[{"name":"The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Handan","family":"Tan","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital of Chongqing Medical University, Chongqing Key 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