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Table 5 Differential methylation in relation to current smoking for genes with transcripts differently expressed (p < 0.05) in relation to smoking pack-years (ordered by chromosomal location)

From: DNA methylation and smoking in Korean adults: epigenome-wide association study

Differentially methylated probes in relation to current smoking compared to never smoking (the Korean COPD cohort) Gene (distance to genec) Differentially expressed genes in relation to pack-years in lung tissue (Asan Biobank)
Differentially methylated probe   
 Chra Probe Coef b P Genomic features CpG island   Transcript Coef P
  1 cg20388635 −0.013 1.3E−05 TSS200, promoter Island YTHDF2 NM_001173128 −0.019 0.047
  2 cg22346073 −0.056 5.1E−08 5′UTR Shelf CLASP1 NM_015282 0.019 7.2E−04
cg19394739 −0.012 3.5E−07 Body, promoter Shore DGUOK NM_080916 −0.079 0.003
cg09059267 −0.099 4.2E−06   Island DNPEP (−15098) NM_012100 −0.021 0.037
  3 cg01870865 −0.045 1.0E−05 TSS200, promoter   TREX1 NM_033629 −0.018 0.023
cg19859270d −0.027 1.0E−07 1st exon   GPR15 e NM_005290 0.013 3.0E−04
  5 cg05575921d −0.203 6.5E−13 Body, enhancer Shore AHRR e NM_001242412 0.004 0.047
cg14817490d −0.078 4.7E−06 Body, promoter, DHS  
cg25648203d −0.079 6.2E−07 Body, enhancer, DHS  
  6 cg23164938 −0.016 9.5E−06 TSS1500 Shore ESR1 NM_000125 0.005 0.012
  7 cg05383910 −0.042 2.1E−06 5′UTR, enhancer   ELMO1 e NR_038121 0.017 0.031
cg20663219 −0.054 9.4E−06 Body, DHS Shelf STX1A NM_001165903 −0.003 0.045
  10 cg20723792 −0.097 4.8E−10 Body, enhancer, DHS   FAM53B NM_014661 0.009 0.042
  11 cg25426350 −0.030 2.5E−06 TSS200   HPX NM_000613 −0.003 0.024
  13 cg17058676 −0.028 2.5E−06 Body Shore CENPJ NM_018451 0.003 0.035
  14 cg16579351 −0.017 1.2E−05 Body   BRF1 NM_001242788 −0.012 0.041
  17 cg13521620 −0.052 1.2E−05 5′UTR Shore YPEL2 NM_001005404 0.019 0.023
Differentially methylated region     
 Chr Region #CpGs FDR Genomic features CpG island     
  1 230415343–230416101 6 0.002 3′UTR Island, shore GALNT2 NM_004481 0.033 0.018
  2 241975756–241976244 4 1.9E−06 Body, promoter, DHS island SNED1 e NM_001080437 0.017 0.014
  3 98250723–98251294 2 6.2E−07 TSS200, 1st exon   GPR15 e NM_005290 0.013 3.0E−04
  3 187870621–187871538 11 1.5E−05 TSS1500, TSS200 Shore, island LPP e NM_005578 0.019 0.018
  5 373378–374425 5 4.6E−17 Body, enhancer Shore, island AHRR e NM_001242412 0.004 0.047
  5 392920–393366 3 5.8E−08 Body, promoter, DHS  
  7 2768988–2770410 5 4.7E−06 3′UTR, enhancer   GNA12 e NM_007353 0.022 0.019
  17 61511069–61511829 4 4.9E−04 3′UTR, body, enhancer Shore, island CYB561 NM_001017916 −0.056 0.005
  1. Genomic features were based on Illumina’s Annotation file and those for DMRs were based on CpGs at start and end position of each region. Categories for the features includes (1) Body, gene body; (2) 5′UTR, 5 prime untranslated region; (3) 3′UTR, 3 prime untranslated region; (4) TSS200, 200 basepair within transcription start site; (5) TSS1500, 1500 basepair within transcription start site; and (6) DHS, DNase I hypersensitivity site
  2. aChromosome
  3. bRegression coefficient from statistical model
  4. cDistance to transcription start site of the mapped gene (basepair, National Center for Biotechnology Information human reference genome assembly Build 37.3)
  5. dProbe identified in previous epigenome-wide association studies (EWASs) of smoking
  6. eGene identified in previous EWASs of smoking