Table 4.

Best meQTL results per MCTD-DMS.

CpG site	CpG position	CpG gene	SNP	Alleles	SNP position	SNP gene	β	P
cg12439472	13:43565399	EPSTI1	rs4142312	GA	13:43574986	EPSTI1	−0.167	2.6 × 10−44
cg09858955	2:58135951	VRK2	rs2678900	GT	2:58177683	VRK2	0.056	3.3 × 10−20
cg07878065	18:2641871	Intergenic	rs9958281	AG	18:2641809	Intergenic	0.019	1.1 × 10−19
cg03879629	3:46152446	Intergenic	rs13085367	CT	3:46172824	Intergenic	0.072	2.7 × 10−18
cg04268125	1:154579384	ADAR	rs9616	TA	1:154555733	ADAR	0.060	7.9 × 10−18
cg23892836	6:29692085	HLA-F	rs2517910	AC	6:29688501	HLA-F	−0.030	4.8 × 10−16
cg17114584	11:613792	IRF7	rs3740648	TG	11:596672	PHRF1	−0.084	4.0 × 10−15
cg00272009	3:122398855	PARP14	rs2668339	CG	3:122392433	PARP14	−0.040	1.1 × 10−14
cg23923934	6:31322914	HLA-B	rs1051488	TC	6:31322911	HLA-B	−0.039	1.3 × 10−14
cg12331471	2:231282369	SP100	rs12694859	TC	2:231254570	SP140L	−0.029	9.2 × 10−14
cg06981309	3:146260954	PLSCR1	rs2738918	CT	3:146257165	PLSCR1	0.039	1.1 × 10−12
cg14864167	8:66751182	PDE7A	rs6472232	GT	8:66792632	PDE7A	−0.048	1.7 × 10−12
cg12110437	8:144098888	LY6E	rs7812819	GA	8:144095249	RP11-273G15.2.	−0.046	1.0 × 10−11
cg23352030	20:62198469	PRIC285	rs9784182	GA	20:62263201	Intergenic	0.054	1.0 × 10−11
cg13755924	21:42791937	MX1	rs78554586	AG	21:42808343	MX1	−0.053	1.9 × 10−11
cg14880222	1:79143979	Intergenic	rs7524036	AC	1:79158657	Intergenic	0.029	1.0 × 10−10
cg08293824	3:172313318	Intergenic	rs234055	GT	3:172310820	RP11-408H1.3	0.038	1.8 × 10−10
cg07839313	19:17514600	BST2	rs12971834	TC	19:17516689	CTD-2521M24.9,/BST2	−0.027	3.8 × 10−10
cg06033320	8:66750110	PDE7A	rs6472232	GT	8:66792632	PDE7A	−0.034	5.4 × 10−10
cg07596065	22:50984393	Intergenic	rs9306547	CT	22:50993225	SYCE3	0.016	8.4 × 10−10
cg12013713	7:139760671	PARP12	rs7805521	AT	7:139761176	PARP12	0.032	7.9 × 10−09
cg09379489	12:12224360	BCL2L14	rs4763773	GA	12:12225613	BCL2L14	−0.024	1.6 × 10−08
cg24603130	18:60253492	ZCCHC2	rs57868717	TC	18:60247316	ZCCHC2	−0.032	2.3 × 10−08
cg16427501	8:145060083	PARP10	rs11136343	GA	8:145058986	PARP10	0.017	4.2 × 10−08
cg26202327	2:233193151	DIS3L2	rs10933388	AT	2:233176366	DIS3L2	−0.035	5.0 × 10−08
cg10734665	15:26107410	ATP10A	rs12908995	AG	15:26015194	ATP10A	−0.025	7.5 × 10−08

Alleles represents the allele tested in first place followed by the non-tested allele for each SNP.

β represents the DNA methylation change in the addition of one allele tested.

P represents the P-value obtained from the linear regression model adjusted by age, sex, batch effects, estimated cell proportions, disease status and first genetic component.

Genomic positions are based on the hg19 human reference sequence build (GRCh37).