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Table 2 CpG sites associated with cardio-metabolic traits in DNA methylation analysis

From: Smoking-related changes in DNA methylation and gene expression are associated with cardio-metabolic traits

CpG Chr:positiona Gene IDb Trait Model 1 Model 2 Replication
Effect P value Effect P value Effect P value
cg04716530 16:30485684 ITGAL HDL 0.01700 2.02E−07 0.01550 6.34E−06 0.00014 9.82E−04
cg07826859 7:45020086 MYO1G HDL 0.01440 6.79E−06 0.01390 3.61E−05 0.00018 1.61E−03
cg26724967 16:3115223 IL32 HDL 0.01290 2.89E−06 0.01220 2.34E−05 0.00015 1.63E−03
cg16391678 16:30485597 ITGAL HDL 0.01520 1.03E−06 0.01400 1.60E−05 0.00013 5.14E−03
cg16519923 16:30485810 ITGAL HDL 0.01980 8.23E−08 0.01790 3.44E−06 0.00012 9.75E−03
cg10310310 7:157367150 PTPRN2;MIR153-2 HDL 0.01130 4.49E−06 0.01060 4.05E−05 0.00011 1.96E−02
cg24323726 3:111314186 ZBED2;CD96 HDL 0.01300 4.84E−07 0.01230 5.32E−06 0.00009 3.41E−02
cg07929642 16:89390685 ANKRD11 HDL 0.01650 1.87E−07 0.01550 3.13E−06 0.00009 4.25E−02
cg21566642 2:233284661 TG − 0.01990 3.89E−05 − 0.02150 1.91E−05 − 0.01967 1.14E−05
cg04716530 16:30485684 ITGAL TG − 0.01370 1.23E−06 −0.01220 3.58E−05 −0.00380 5.34E−04
cg27409015 2:158114424 GALNT5 TG 0.01660 8.39E−07 0.01490 2.16E−05 0.00683 1.50E−03
cg06635952 2:70025869 ANXA4 TG 0.01300 9.06E−07 0.01280 3.36E−06 0.00502 5.95E−03
cg11095027 11:1297066 TOLLIP TG 0.00996 2.72E−05 0.01040 2.64E−05 0.00375 7.82E−03
cg26219092 8:134388022 TG 0.01050 2.37E−06 0.00991 2.05E−05 0.00285 1.73E−02
cg10919522 14:74227441 C14orf43 TG − 0.01410 7.90E−09 − 0.01260 7.97E−07 − 0.00491 1.91E−02
cg22635096 21:46550644 ADARB1 TG 0.01370 6.61E−08 0.01300 8.65E−07 0.00392 3.55E−02
cg00310412 15:74724918 SEMA7A WHR − 0.05000 3.96E−05 − 0.07150 1.95E−07 − 0.06952 4.54E−05
cg04424621 6:27101941 HIST1H2BJ WHR − 0.06490 1.06E−05 − 0.07360 1.03E−05 − 0.07191 5.73E−05
cg04583842 16:88103117 BANP WHR 0.12600 5.29E−08 0.12500 1.56E−06 0.06802 3.71E−03
cg13755776 11:3602845 WHR − 0.08530 1.03E−06 − 0.08200 3.33E−05 − 0.04521 3.71E−02
cg17287155 5:393347 AHRR BMI 0.00117 8.69E−06 NA NA 0.00053 3.11E−06
cg26361535 8:144576604 ZC3H3 BMI 0.00155 1.85E−07 NA NA 0.00102 2.38E−05
cg06096336 2:231989800 PSMD1;HTR2B BMI 0.00168 9.51E−07 NA NA 0.00111 1.66E−04
cg13708645 12:121974305 KDM2B BMI 0.00152 6.72E−07 NA NA 0.00089 1.01E−03
cg25649826 17:20938740 USP22 BMI 0.00086 1.63E−05 NA NA 0.00041 3.15E−03
cg24539517 10:121161258 GRK5 BMI 0.00149 2.95E−05 NA NA 0.00078 4.33E-03
cg03636183 19:17000585 F2RL3 BMI 0.00160 3.04E−05 NA NA 0.00063 3.40E−02
  1. The table shows 26 CpGs that are associated to at least one cardio-metabolic trait and in eQTM with at least one smoking-related gene-expression probe
  2. Only CpGs significantly associated in both models and nominally significant (P < 0.05) in the replication are presented in this table
  3. HDL high-density lipoprotein, TG triglycerides, WHR waist to hip ratio, BMI body mass index, NA not applicable (because of adjusting for BMI)
  4. Model 1: Adjusted for age, sex, cell count, and technical covariates. Model 2: Model 1 + BMI and relevant medication
  5. We did not correct for additional covariates when testing the association for BMI
  6. P value threshold for discovery P < 4.08 × 10–5 (0.05/1224)
  7. P value threshold for replication: HDL, P < 8.62 × 10–4 (0.05/58); TG, P < 1.43 × 10–3 (0.05/35); WHR, P < 8.33 × 10–3 (0.05/6); BMI, P < 3.13 × 10–3 (0.05/16)
  8. CpGs that are presented underlined passed the replication P value threshold in 1727 participants of the KORA study
  9. aGenome coordinates provided by Illumina (GRCh37/hg19)
  10. bAccording to the Illumina Infinium HumanMethylation450K annotation file