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Table 3 The selected candidate CpG sites by epigenome-wide association (EWA) scan on persistent cocaine use (n = 467) and HIV severity (n = 875)

From: DNA methylation mediates the effect of cocaine use on HIV severity

CpG

Chr

Position

Nearest gene

Cocaine EWA effect size

Cocaine EWA p value

VACS index EWA effect size

VACS index EWA p value

Reference gene group

Relations to CpG islands

cg22917487

3

39322103

CX3CR1

1.71E−02

1.69E−07

1.96E−04

1.73E−03

Body;TSS200;5UTR;TSS1500

 

cg07839457

16

57023022

NLRC5

− 5.18E−02

3.16E−05

− 7.08E−04

4.02E−04

TSS1500

N_Shore

cg26312951

21

42797847

MX1

− 3.93E−02

3.24E−05

− 7.80E−04

2.50E−07

TSS200;5UTR

N_Shore

cg06188083

10

91093005

IFIT3

− 5.06E−02

3.34E−05

− 9.96E−04

4.76E−08

Body

 

cg08122652

3

1.22E+08

PARP9

− 6.13E−02

1.10E−04

− 1.26E−03

2.30E−10

5UTR;TSS1500

N_Shore

cg22385827

2

2.11E+08

C2orf67

8.10E−03

2.01E−04

1.20E−04

7.52E−04

TSS1500

Island

cg22930808

3

1.22E+08

PARP9

− 6.52E−02

2.44E−04

− 1.17E−03

1.52E−06

5UTR;TSS1500

N_Shore

cg06981309

3

1.46E+08

PLSCR1

− 4.29E−02

2.63E−04

− 5.72E−04

4.21E−04

5UTR

N_Shore

cg03753191

13

43566902

EPSTI1

− 1.36E−02

2.81E−04

− 2.44E−04

5.50E−05

TSS1500

S_Shore

cg00096307

2

1.07E+08

UXS1

− 1.12E−02

3.59E−04

1.74E−04

5.73E−04

Body

 

cg26396492

20

19915762

RIN2

− 1.26E−02

4.76E−04

− 2.00E−04

9.15E−04

Body

 

cg22940798

6

32805554

TAP2

− 1.93E−02

4.82E−04

− 2.89E−04

4.72E−04

Body

N_Shore

cg08623256

5

3858275

 

− 1.73E−02

6.96E−04

3.17E−04

7.18E−04

 

S_Shelf

cg08818207

6

32820355

TAP1

− 2.67E−02

8.18E−04

− 6.18E−04

2.11E−07

Body

N_Shore

cg03038262

11

315262

IFITM1

− 2.98E−02

9.59E−04

− 6.46E−04

7.65E−09

3UTR

N_Shore

  1. VACS index Veteran Aging Cohort Study index