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Both genetic and environmental risk factors contribute to ischemic stroke, but the underlying epigenetic mechanisms which mediate genetic and environmental risk effects are not fully understood. The aim of this study was to explore whether DNA methylation loci located in the ATP-binding cassette G1 (<jats:italic>ABCG1<\/jats:italic>) and apolipoprotein E (<jats:italic>APOE<\/jats:italic>) genes, both involved in the metabolism of lipids in the body, are related to ischemic stroke, using the Fangshan\/Family-based Ischemic Stroke Study in China. We also tested if these CpG sites were associated with early signs of cardiovascular atherosclerosis (carotid intima\u2013media thickness (cIMT), ankle\u2013brachial index (ABI), and brachial\u2013ankle pulse wave velocity (baPWV)).<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>DNA methylation at the cg02494239 locus in <jats:italic>ABCG1<\/jats:italic> was correlated with ischemic stroke after adjusting for gender, previous history of diabetes and hypertension, smoking, drinking, body mass index, and blood lipid levels (above vs below mean, OR = 2.416, 95% CI 1.024\u20135.700, <jats:italic>P<\/jats:italic> = 0.044; 75\u2013100% percentile vs 0\u201325% percentile, OR = 4.461, 95% CI 1.226\u201316.225, <jats:italic>P<\/jats:italic> = 0.023). No statistically significant associations were observed for the cg06500161 site in <jats:italic>ABCG1<\/jats:italic> and the cg14123992 site in <jats:italic>APOE<\/jats:italic> with ischemic stroke. The study detected that hypermethylation of the <jats:italic>ABCG1<\/jats:italic> gene was significantly associated with cIMT, hypermethylation of the <jats:italic>APOE<\/jats:italic> gene was significantly related to ABI, and methylation of the <jats:italic>APOE<\/jats:italic> gene was statistically negatively correlated with baPWV. The above relationships demonstrated gender differences.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>These findings suggest that epigenetic modification of <jats:italic>ABCG1<\/jats:italic> and <jats:italic>APOE<\/jats:italic> may play a role in the pathway from disturbed blood lipid levels to the development of cardiovascular diseases. Future prospective validation of these findings is warranted.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s13148-019-0784-0","type":"journal-article","created":{"date-parts":[[2019,12,10]],"date-time":"2019-12-10T12:04:28Z","timestamp":1575979468000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":34,"title":["Overall and sex-specific associations between methylation of the ABCG1 and APOE genes and ischemic stroke or other atherosclerosis-related traits in a sibling study of Chinese population"],"prefix":"10.1186","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3271-8618","authenticated-orcid":false,"given":"Xueying","family":"Qin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jin","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yiqun","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xun","family":"Tang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pei","family":"Gao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lin","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengying","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yao","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaowen","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dafang","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yonghua","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,12,10]]},"reference":[{"issue":"5439","key":"784_CR1","doi-asserted-by":"publisher","first-page":"481","DOI":"10.1126\/science.286.5439.481","volume":"286","author":"AP Wolffe","year":"1999","unstructured":"Wolffe AP, Matzke MA. 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