A variability in response of osteoclasts to zoledronic acid is mediated by smoking-associated modification in the DNA methylome

Tan, Qihua; Møller, Anaïs Marie Julie; Qiu, Chuan; Madsen, Jonna Skov; Shen, Hui; Bechmann, Troels; Delaisse, Jean-Marie; Kristensen, Bjarne Winther; Deng, Hong-Wen; Karasik, David; Søe, Kent

doi:10.1186/s13148-023-01449-1

Table 2 The 59 CpGs showing significant smoking-dependent association between IC50 and DNA methylation

From: A variability in response of osteoclasts to zoledronic acid is mediated by smoking-associated modification in the DNA methylome

Locus	CpG ID	Coefficient	t-value	p-value	Chr	Position	FDR	Gene	BMD association*
1	cg03009196	9.97E−06	6.35	1.20E−06	1	60,392,511	0.022	CYP2J2	Yes
2	cg22010000	− 1.01E−05	− 8.55	6.89E−09	1	151,738,555	0.002	OAZ3	Yes
3	cg08901901	8.25E−06	8.04	2.14E−08	1	160,951,907	0.002		No
4	cg25619551	− 9.25E−06	− 6.59	6.62E−07	1	193,710,042	0.015		No
5	cg15073625	− 5.60E−06	− 5.88	3.90E−06	2	23,862,014	0.047	KLHL29	Yes
6	cg10565322	− 8.49E−06	− 6.46	9.15E−07	2	43,136,493	0.017		Yes
7	cg17641218	− 9.64E−06	− 7.78	3.87E−08	2	85,804,603	0.002	VAMP8	Yes
8	cg02494004	− 8.62E−06	− 6.35	1.21E−06	2	147,162,808	0.022		Yes
9	cg06342954	− 8.24E−06	− 6.34	1.24E−06	2	236,757,889	0.022	AGAP1	Yes
10	cg14485214	− 7.96E−06	− 7.23	1.42E−07	2	241,957,552	0.005	SNED1	Yes
11	cg00227784	− 7.62E−06	− 8.76	4.33E−09	3	126,391,755	0.002		Yes
12	cg14379327	− 6.77E−06	− 7.54	6.87E−08	4	146,404,134	0.003	SMAD1	Yes
13	cg20093868	− 8.86E−06	− 5.85	4.27E−06	4	152,646,689	0.049	GATB	No
14	cg09865379	− 7.61E−06	− 5.94	3.35E−06	4	165,708,173	0.042	LINC01207	No
15	cg06753918	− 5.91E−06	− 6	2.89E−06	5	6,182,215	0.038		No
16	cg16653901	− 9.45E−06	− 6.27	1.48E−06	5	133,513,511	0.025	SKP1	No
17	cg01247535	1.03E−05	6.72	4.89E−07	6	15,418,354	0.012	JARID2	No
18	cg17866778	− 1.58E−05	− 6.51	8.05E−07	6	26,233,442	0.017		Yes
19	cg06501109	− 1.23E−05	− 6.08	2.37E−06	6	30,850,309	0.033	DDR1	Yes
20	cg17774634	− 9.25E−06	− 7.83	3.45E−08	6	97,730,494	0.002	C6orf167;MIR548H3	No
21	cg05923369	− 1.04E−05	− 6.47	8.93E−07	7	2,251,548	0.017	MAD1L1	No
22	cg24648241	− 9.54E−06	− 5.98	3.01E−06	7	38,347,775	0.039		No
23	cg14355428	− 9.62E−06	− 8.56	6.76E−09	7	91,762,876	0.002	CYP51A1	Yes
24	cg02396891	− 6.61E−06	− 6.3	1.36E−06	7	93,222,734	0.023		No
25	cg10333170	− 9.21E−06	− 5.91	3.66E−06	7	134,521,311	0.046	CALD1	No
26	cg22859658	− 2.03E−05	− 7.77	4.00E−08	7	144,422,735	0.002	TPK1	No
27	cg10993470	− 1.05E−05	− 6.03	2.66E−06	8	55,533,939	0.036	RP1	No
28	cg23855920	− 9.03E−06	− 6.24	1.58E−06	8	103,764,916	0.026		No
29	cg24529650	− 1.02E−05	− 7.24	1.38E−07	9	14,031,418	0.005		No
30	cg13396858	− 1.05E−05	− 5.89	3.85E−06	9	134,249,466	0.047		Yes
31	cg00013660	− 8.96E−06	− 7.6	5.95E−08	9	140,068,770	0.003		Yes
32	cg12368066	− 1.37E−05	− 6.93	2.88E−07	10	9,449,275	0.008		No
33	cg00762372	− 6.16E−06	− 6.19	1.79E−06	10	25,618,736	0.027	GPR158	No
34	cg13820475	− 9.93E−06	− 6.46	9.19E−07	10	44,461,659	0.017	LINC00841	No
35	ch.10.107354959F	− 9.33E−06	− 6.53	7.69E−07	10	107,364,969	0.017		No
36	cg02701677	− 8.07E−06	− 7.46	8.30E−08	11	23,970,707	0.003		No
37	cg08086799	− 1.20E−05	− 6.9	3.12E−07	11	62,495,467	0.009	TTC9C;HNRNPUL2	Yes
38	cg22968863	− 1.03E−05	− 7.51	7.23E−08	11	72,441,739	0.003	ARAP1	No
39	cg20199739	1.88E−05	7.03	2.30E−07	11	107,730,522	0.007	SLC35F2	No
40	cg04932413	− 1.54E−05	− 6.76	4.33E−07	14	103,002,828	0.011	KLC1	Yes
41	cg01279902	− 1.01E−05	− 8.12	1.79E−08	14	104,171,040	0.002	XRCC3	Yes
42	cg04662961	− 6.63E−06	− 6.11	2.21E−06	15	44,486,562	0.031	FRMD5	Yes
43	cg27111704	− 7.75E−06	− 6.52	7.95E−07	15	83,847,628	0.017	HDGFRP3	No
44	cg16362027	− 7.71E−06	− 5.86	4.10E−06	15	88,856,288	0.048		No
45	cg22581270	− 7.20E−06	− 7.01	2.39E−07	16	3,193,156	0.007	CASP16P	Yes
46	cg03660158	9.88E−06	6.19	1.77E−06	16	57,769,342	0.027	KATNB1	Yes
	cg00122310	1.30E−05	7.79	3.84E−08	16	57,769,432	0.002
	cg00439196	1.48E−05	8.09	1.93E−08	16	57,769,757	0.002
	cg06830769	1.14E−05	8.07	2.02E−08	16	57,769,885	0.002
47	cg21854895	− 1.06E−05	− 7.92	2.81E−08	17	71,305,638	0.002	CDC42EP4	Yes
48	cg06400109	8.45E−06	6.18	1.83E−06	17	76,183,118	0.027	AFMID;TK1	Yes
	cg07246050	8.44E−06	6.86	3.44E−07	17	76,183,123	0.009	AFMID;TK1
49	cg21441526	− 9.09E−06	− 7.46	8.11E−08	18	21,516,439	0.003	LAMA3	No
50	cg26258423	− 7.60E−06	− 6.22	1.67E−06	18	75,380,233	0.027		No
51	cg27071707	− 7.31E−06	− 7.83	3.49E−08	19	1,614,334	0.002	TCF3	Yes
52	cg18788725	− 7.34E−06	− 6.07	2.40E−06	19	45,512,122	0.033	RELB	No
53	cg04700648	− 1.03E−05	− 6.14	2.01E−06	19	52,888,958	0.029	ZNF880	No
54	cg05325193	8.85E−06	6.86	3.47E−07	20	22,558,233	0.009	C20orf56	No
55	cg25580335	− 9.10E−06	− 7.1	1.93E−07	22	24,738,240	0.006	SPECC1L	No

*CpG associated with BMD at q < 0.05 within 5 Kb of this locus

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ISSN: 1868-7083

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