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Table 3 Gene expression probes associated with cardio-metabolic traits

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

Probe ID Gene IDa Chr. a Trait Model 1 Model 2 Replication
Effect P value Effect P value Effect P value
ILMN_1700306 OCIAD2 4 HDL − 0.4114 8.39E−07 − 0.3573 5.15E−05 − 0.0040 9.20E−05
ILMN_1761463 EFHD2 1 HDL 0.4668 1.60E−07 0.3576 0.00013 0.0022 1.38E−03
ILMN_2261416 CD3D 11 TG 0.9089 2.22E−15 0.8328 3.84E−12 0.3233 2.58E−15
ILMN_2079655 KLRB1 12 TG 1.1666 6.48E−14 1.0518 1.01E−10 0.3946 4.09E−15
ILMN_1779324 GZMA 5 TG 1.0562 1.99E−09 1.0033 6.01E−08 0.2734 2.06E−13
ILMN_1761463 EFHD2 1 TG − 0.4238 2.59E−09 − 0.3434 3.54E−06 − 0.1298 9.99E−13
ILMN_1700306 OCIAD2 4 TG 0.3413 3.32E−07 0.2998 1.93E−05 0.1691 7.64E−10
ILMN_1808939 RPS6 9 TG 0.6145 5.58E−11 0.5687 7.54E− 09 0.3001 1.17E−09
ILMN_1812191 C12orf57 12 TG 0.4392 1.37E−05 0.3897 0.00023 0.1772 1.07E−07
ILMN_1776181 BIRC3 11 TG 0.6940 2.86E−10 0.6176 8.34E−08 0.1473 4.89E−07
ILMN_1813836 DARS 2 TG 0.2657 9.37E−07 0.2878 4.67E−07 0.0894 3.18E-06
ILMN_1669927 ICOS 2 TG 0.2859 6.88E-06 0.2692 5.75E-05 0.0925 2.95E−04
ILMN_2198878 INPP4B 4 TG 0.2950 2.99E−07 0.2853 2.53E−06 0.0668 5.93E−04
ILMN_2366041 ITM2C 2 TG − 0.5648 6.81E−09 − 0.4159 3.35E−05 − 0.0818 6.33E−03
ILMN_1680453 ITM2C 2 TG − 0.5880 5.50E−08 − 0.4295 0.000124 − 0.0818 7.05E−03
ILMN_2352563 CLDND1 3 TG 0.3877 4.61E−05 0.4003 6.52E−05 0.0656 3.53E−02
ILMN_2079655 KLRB1 12 Insulin 0.7694 7.01E−09 0.6393 5.21E−05 0.2120 5.59E−05
ILMN_1766657 STOM 9 BMI 0.0549 3.85E−07 NA NA 0.0196 2.56E−08
ILMN_1671891 PID1 2 BMI − 0.0425 7.23E−09 NA NA − 0.0137 3.27E−06
ILMN_2366041 ITM2C 2 BMI − 0.0577 1.86E−09 NA NA − 0.0123 9.53E−05
ILMN_1773650 LRRN3 7 BMI − 0.0669 3.77E−05 NA NA − 0.0162 1.70E−03
ILMN_1661599 DDIT4 10 BMI − 0.0658 2.75E−07 NA NA − 0.0096 4.06E−03
ILMN_2048591 LRRN3 7 BMI − 0.0604 1.46E−05 NA NA − 0.0086 6.95E−03
ILMN_2377669 CD247 1 BMI − 0.0370 5.95E−05 NA NA − 0.0058 8.01E−03
ILMN_2109197 EPB41L3 18 BMI − 0.0322 0.000112 NA NA − 0.0072 1.12E−02
ILMN_2261416 CD3D 11 BMI 0.0458 6.47E−05 NA NA 0.0107 1.37E−02
ILMN_2079655 KLRB1 12 BMI 0.0669 1.63E−05 NA NA 0.0122 2.29E–−02
ILMN_1761463 EFHD2 1 BMI − 0.0339 1.46E−06 NA NA − 0.0038 4.68E−02
  1. The table shows 21 probes annotated to 19 genes that are significantly associated with cardio-metabolic traits and in eQTM with at least one smoking-related CpG
  2. Only probes 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, BMI body mass index, NA not applicable (because of adjusting for BMI)
  4. Model 1: Adjusted for age, sex, cell count, RNA quality score, 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 P < 2.25 × 10–4 (0.05/200)
  7. P value threshold for replication: HDL, P < 0.01, (0.05/5); TG, P < 3.33 × 10–3 (0.05/15); Insulin, P < 0.03 (0.05/2); BMI, P < 3.13 × 10–3 (0.05/16)
  8. Genes that are presented underlined passed the replication p value threshold in 687 participants of the KORA study
  9. aAccording to the by Illumina provided annotation file