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Table 4 The DNA methylation sites associated with gene

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

Gene expressiona Trait DNA methylationb eQTMc
ProbeID Effect P value CpG Effect P value Coeff P value
ILMN_1779324 (GZMA) 1.0033 6.01E−08 TG cg04716530 − 0.0122 3.58E−05 − 11.7641 6.91E−12
ILMN_2352563 (CLDND1) 0.4003 6.52E−05 TG cg21566642 − 0.0215 1.91E−05 − 5.1957 3.54E−19
ILMN_1671891 (PID1) − 0.0425 7.23E−09 BMI cg03636183 0.0016 3.04E−05 − 3.9797 1.28E−11
ILMN_1773650 (LRRN3) − 0.0669 3.77E−05 BMI cg03636183 0.0016 3.04E−05 − 16.4622 3.46E−41
     cg06096336 0.0017 9.51E−07 − 15.0031 2.91E−24
     cg13708645 0.0015 6.72E−07 − 9.5025 2.31E−09
     cg17287155 0.0012 8.69E−06 − 26.2306 3.09E−54
     cg25649826 0.0009 1.63E−05 − 14.4989 3.43E−08
     cg26361535 0.0016 1.85E−07 − 12.549 2.30E - 11
ILMN_2048591 ( LRRN3) − 0.0604 1.46E−05 BMI cg03636183 0.0016 3.04E−05 − 14.4435 2.67E−43
     cg06096336 0.0017 9.51E−07 − 11.5428 1.40E−19
     cg13708645 0.0015 6.72E−07 − 8.2627 1.36E−09
     cg17287155 0.0012 8.69E−06 − 21.4408 1.19E−48
  1. The table shows an overview of the overlap of the hits with nominal significant (P < 0.05) replication in KORA in all three association analyses, including the association between (1) DNA methylation and cardio-metabolic traits, (2) gene expression and cardio-metabolic traits, and (3) the eQTM results for the gene and CpG that are associated with the same cardio-metabolic trait
  2. P value thresholds in the discovery for DNA methylation P < 4.08 × 10–5 (0.05/1224), gene expression P < 2.25 × 10–4 (0.05/200) and for eQTM P < 4.4 × 10–8 (0.05/443 × 2549)
  3. P value thresholds in the replication for TG; gene expression P < 3.33 × 10–3 (0.05/15), DNA methylation P < 1.43 × 10–3 (0.05/35), and BMI; gene expression
  4. P < 3.13 × 10–3 (0.05/16), DNA methylation P < 3.13 × 10–3 (0.05/16), and eQTM P < 2.04 × 10–7 (0.05/1224 × 200)
  5. Results that are presented underlined passed the replication P value threshold in the KORA study
  6. TG triglycerides, BMI body mass index
  7. aExpression probe ~ cardio-metabolic trait + age, sex, cell count, RNA quality score, technical covariates, BMI and relevant medication
  8. bCpGs ~ cardio-metabolic trait + age, sex, cell count, technical covariates, BMI and relevant medication
  9. cExpression probe ~ CpGs + age, sex