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Table 3 Methylation-gene expression correlations of the plasma copper-related CpGs (p Value < 1 × 10−5)

From: Profile of copper-associated DNA methylation and its association with incident acute coronary syndrome

CpGs Gene expression probes Methylation–expression correlations
CHR CpG Expression probe Gene Expression rate Relation to gene Effect p-Value FDR
1 cg25112191 ILMN_1771126 RORC 51.39% 1stExon;5′UTR 1.67 (3.01) 0.58 0.76
1 cg25112191 ILMN_1734366 RORC 84.72% 1stExon;5′UTR 1.64 (2.22) 0.74 0.84
1 cg25112191 ILMN_1680399 KIAA1026 65.28% < 50 kb − 7.51 (2.20) 9.83 × 10–4 3.71 × 10–3
1 cg25112191 ILMN_1770927 KIAA1026 87.50% < 50 kb − 7.43 (2.05) 4.33 × 10–4 1.84 × 10–3
1 cg25112191 ILMN_1798458 KIAA1026 95.83% < 50 kb − 7.19 (1.98) 3.91 × 10–4 2.22 × 10–3
1 cg25112191 ILMN_1792726 TDRKH 36.81% < 50 kb 1.15 (2.76) 0.68 0.82
2 cg11023668 ILMN_1676893 ADCY3 100.00% Body − 0.51 (0.92) 0.58 0.73
2 cg20995564 ILMN_1688698 ZEB2 100.00% Body 1.39 (1.26) 0.27 0.46
3 cg21945842 ILMN_1670870 ALCAM 100.00% TSS1500 3.25 (3.58) 0.37 0.57
5 cg24805089 ILMN_2357015 GRK6 100.00% Body − 2.42 (4.28) 0.57 0.78
5 cg24805089 ILMN_1681802 GRK6 100.00% Body 0.68 (4.37) 0.88 0.97
7 cg21852842 ILMN_2358069 MAD1L1 100.00% Body 3.14 (1.73) 0.07 0.19
8 cg18734877 ILMN_1732318 PTK2B 100.00% Body 5.44 (2.21) 0.01 0.05
8 cg18734877 ILMN_2330966 PTK2B 100.00% Body 3.51 (2.18) 0.11 0.23
8 cg18734877 ILMN_1698849 CHRNA2 82.64% < 50 kb 0.15 (2.53) 0.95 0.98
8 cg18734877 ILMN_1709237 EPHX2 100.00% < 50 kb − 2.03 (2.19) 0.35 0.57
16 cg07798295 ILMN_1709439 CHMP1A 100.00% Body − 2.63 (3.67) 0.47 0.67
19 cg18608055 ILMN_1808811 SBNO2 100.00% Body 7.28 (1.81) 9.53 × 10–5 6.48 × 10–4
19 cg18608055 ILMN_1734353 GPX4 100.00% < 50 kb − 10.28 (1.78) 4.48 × 10–8 7.62 × 10–7
19 cg18608055 ILMN_2378952 GPX4 100.00% < 50 kb − 10.57 (1.77) 1.84 × 10–8 6.26 × 10–7
19 cg18608055 ILMN_1811392 HMHA1 100.00% < 50 kb 9.28 (1.79) 7.40 × 10–7 8.39 × 10–6
19 cg18608055 ILMN_3239240 POLR2E 100.00% < 50 kb 0.78 (1.97) 0.69 0.81
19 cg26470501a ILMN_1710514 BCL3 100.00% Body − 3.77 (2.55) 0.14 0.27
20 cg24263062a ILMN_3261292 EBF4 90.97% Body 2.01 (1.33) 0.14 0.27
20 cg24263062 ILMN_1712046 CPXM1 66.67% < 50 kb 2.57 (1.49) 0.09 0.21
20 cg05825244a ILMN_3261292 EBF4 90.97% Body 1.25 (0.73) 0.09 0.21
20 cg05825244 ILMN_1712046 CPXM1 66.67% < 50 kb 2.06 (0.82) 0.01 0.04
20 cg01523712 ILMN_1746031 RIMS4 59.44% Body 1.80 (2.39) 0.45 0.67
22 cg09349128 ILMN_1782129 ZBED4 100.00% < 50 kb 10.42 (2.88) 4.20 × 10–4 2.04 × 10–3
22 cg09349128 ILMN_1743995 ALG12 97.22% < 50 kb − 0.14 (3.00) 0.96 0.96
22 cg09349128 ILMN_1748707 CRELD2 100.00% < 50 kb − 0.20 (2.97) 0.95 1.00
22 cg09349128 ILMN_1672034 PIM3 48.95% < 50 kb − 5.22 (3.86) 0.18 0.33
22 cg09349128 ILMN_1707748 PIM3 100.00% < 50 kb − 12.08 (2.76) 2.34 × 10–5 1.99 × 10–4
22 cg09349128 ILMN_1789781 PIM3 88.11% < 50 kb − 7.22 (3.04) 0.02 0.06
  1. Methylation–expression correlations were calculated using linear regressions in which inverse normal transformed expression values were regressed on original methylation values adjusted for age and gender. The significant threshold of methylation–expression associations was set at FDR < 0.05
  2. aDNA methylation level of cg26470501 was reported to associated with expression of BCL3 gene; DNA methylation level of cg24263062 and cg05825244 was reported to positively associated with EBF4 gene in public database (FDR < 0.05) (https://www.genenetwork.nl/biosqtlbrowser/)
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