Table 5.

Top Methylation Probes (CpGs)∗ That Are in Transcription Regulatory Elements (TREs) in the Promoter or Enhancer Regions of Genes That Are Differentially Expressed in Atopic Asthma

Chr	Probe	Pos	Gene	TRE Start	TRE End	Effect size	eQTM P	EWAS P	TWAS P
Promoter
6	cg11210880	11779911	ADTRP	11779280	11781280	-0.43	1.1 × 10-12	7.6 × 10-9	4.0 × 10-11
1	cg01062020	162382848	SH2D1B	162381928	162383928	-0.2	1.7 × 10-6	2.0 × 10-6	9.8 × 10-11
20	cg20895028	58533443	CDH26	58531470	58533470	-0.49	6.0 × 10-6	4.2 × 10-10	1.5 × 10-10
17	cg18105842	7341440	FGF11	7339591	7341591	-0.23	3.6 × 10-9	8.5 × 10-7	1.5 × 10-10
20	cg01352551	19191994	SLC24A3	19191289	19193289	-0.33	8.1 × 10-8	1.5 × 10-4	1.7 × 10-10
2	cg14499385	190446494	SLC40A1	190445537	190447537	0.48	1.3 × 10-10	6.6 × 10-4	3.9 × 10-10
13	cg18341491	38174258	POSTN	38172981	38174981	-0.7	2.9 × 10-8	6.3 × 10-7	8.2 × 10-10
17	cg13606025	68070495	KCNJ16	68069365	68071365	-0.45	7.8 × 10-10	2.5 × 10-4	1.9 × 10-9
3	cg13705284	58523313	ACOX2	58522929	58524929	-0.45	4.0 × 10-18	8.8 × 10-10	3.8 × 10-9
10	cg19571004	135340850	CYP2E1	135338866	135340866	-0.49	5.2 × 10-21	3.3 × 10-6	3.9 × 10-9
17	cg25170091	202716	RPH3AL	202633	204633	-0.21	7.9 × 10-15	4.6 × 10-6	5.2 × 10-9
5	cg00049323	472564	LOC100288152	471350	473350	0.18	9.5 × 10-7	1.0 × 10-13	6.0 × 10-9
7	cg23468130	114562060	MDFIC	114560208	114562208	-0.28	1.1 × 10-7	2.2 × 10-4	9.1 × 10-9
8	cg10054641	133773093	TMEM71	133772914	133774914	-0.2	1.0 × 10-12	1.6 × 10-11	1.9 × 10-8
3	cg08450017	45984838	CXCR6	45982972	45984972	-0.46	2.0 × 10-32	1.8 × 10-6	2.5 × 10-8
Enhancer
3	cg22012981	58522689	ACOX2	58520920	58522840	-0.86	3.1 × 10-31	2.0 × 10-11	3.8 × 10-9
16	cg16219266	67433184	FBXL8	67432850	67433250	-0.4	3.3 × 10-6	1.1 × 10-5	1.2 × 10-8
17	cg04204452	1479213	MYO1C	1479060	1479890	0.2	3.9 × 10-8	4.4 × 10-6	1.4 × 10-8
16	cg16219266	67433184	NOL3	67432850	67433250	-0.34	1.0 × 10-5	1.1 × 10-5	2.3 × 10-8
3	cg16209444	58522771	KCTD6	58520920	58522840	-0.29	1.0 × 10-9	1.1 × 10-8	3.0 × 10-8
11	cg15453278	67134607	RHOD	67133100	67134930	-0.14	1.7 × 10-5	5.1 × 10-5	1.9 × 10-7
7	cg20813462	2646259	TTYH3	2645630	2646750	-0.18	1.5 × 10-6	2.4 × 10-3	3.9 × 10-7
17	cg04204452	1479213	ABR	1479060	1479890	0.15	3.5 × 10-7	4.4 × 10-6	4.2 × 10-7
7	cg20813462	2646259	SNX8	2645630	2646750	-0.15	1.5 × 10-6	2.4 × 10-3	6.3 × 10-7
16	cg07261196	75601025	KARS	75600810	75601930	0.16	2.1 × 10-5	5.3 × 10-4	4.2 × 10-6
17	cg01780984	79058859	BAIAP2	79058690	79059450	-0.26	1.4 × 10-8	7.8 × 10-4	1.4 × 10-5
12	cg24437859	7066614	PTMS	7065730	7066810	0.16	9.0 × 10-6	6.9 × 10-5	2.1 × 10-5
17	cg04204452	1479213	SERPINF2	1479060	1479890	0.37	5.1 × 10-14	4.4 × 10-6	2.4 × 10-5
16	cg16219266	67433184	TRADD	67432850	67433250	0.53	2.5 × 10-6	1.1 × 10-5	8.6 × 10-5
6	cg19053046	33048254	HLA-DPA1	33046460	33048440	-0.34	6.8 × 10-15	3.2 × 10-4	8.6 × 10-5

The top 15 methylation-gene pairs are presented for each category (promoter or enhancer region). Results sorted by TWAS P value.²⁹ A total of 143 mediation paths in the promoter region of the associated genes and 29 mediation paths in the enhancer region (lung) of the associated genes were identified. Only one mediation path was presented per gene. Mediation analysis was conducted using Baron and Kenny (1986).⁹