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Table 1 Cox regression analysis: Hazard Ratio (HR) for the development of arsenic-induced skin lesions by presence or absence of genomic deletions in different chromosomal locations. Combined analysis of total 2171 HEALS participants. Top genomic segments are sorted by chromosome

From: Association between genome-wide copy number variation and arsenic-induced skin lesions: a prospective study

CNV genomic coordinates (GRCh37/hg19)

cytoband

length (bps)

Freq_Del

Nearest Gene

Distance to Nearest Gene (bps)b

HR (gene)a

95% CI (gene)

p-value

Bonferroni p-value

Nearest reported CNV in DGV database

Distance to Nearest reported CNV (bps)c

chr2:104,543,558-104,558,092

2q12.1

14,535

18.06%

RP11-76I14.1 (+)

0

1.70

1.36

2.13

4.35E-06

0.005

chr2:104,593,605..104760102

35,513

chr2:104,558,092-104,568,449

2q12.1

10,358

18.06%

RP11-76I14.1 (+)

0

1.70

1.36

2.13

4.11E-06

0.005

chr2:104,593,605..104760102

25,156

chr2:104,573,423-104,581,271

2q12.1

7849

18.70%

RP11-76I14.1 (+)

0

1.67

1.34

2.10

7.05E-06

0.008

chr2:104,593,605..104760102

12,334

chr3:102,717,330-102,770,447

3q12.3

53,118

6.54%

RNU1-43P (+)

108,357

2.11

1.53

2.91

5.08E-06

0.006

chr3:102,743,602..102752706

0

chr5:164,917,182-164,925,967

5q34

8786

5.62%

CTC-535 M15.2 (+)

0

2.15

1.55

2.98

4.62E-06

0.005

chr5:164,849,860..164874815

42,367

chr5:164,925,967-164,939,621

5q34

13,655

5.80%

CTC-535 M15.2 (+)

0

2.11

1.52

2.91

6.55E-06

0.007

chr5:164,849,860..164874815

51,152

chr5:164,939,621-164,956,122

5q34

16,502

5.85%

CTC-535 M15.2 (+)

0

2.10

1.52

2.90

7.39E-06

0.008

chr5:164,849,860..164874815

64,806

chr5:164,956,122-164,973,175

5q34

17,054

5.62%

CTC-535 M15.2 (+)

0

2.14

1.54

2.97

5.08E-06

0.006

chr5:164,849,860..164874815

81,307

chr7:151,708,046-151,713,498

7q36.1

5453

8.15%

GALNTL5 (+)

0

1.88

1.40

2.53

3.07E-05

0.035

chr7:151,794,196..151797877

80,698

chr7:151,713,498-151,719,077

7q36.1

5580

7.97%

GALNTL5 (+)

0

1.87

1.39

2.52

4.25E-05

0.048

chr7:151,794,196..151797877

75,119

chr7:62,764,248-62,830,796

7q11.21

66,549

15.98%

VN1R31P (−)

0

1.69

1.34

2.14

1.19E-05

0.014

chr7:62,830,337..62835635

0

chr7:62,835,371-62,889,537

7q11.21

54,167

15.80%

RP11-73B2.2 (−)

0

1.70

1.34

2.15

1.01E-05

0.012

chr7:62,864,828..62908102

0

chr7:62,889,537-62,990,599

7q11.21

101,063

16.12%

PHKG1P2 (+)

0

1.70

1.35

2.15

9.35E-06

0.011

chr7:62,985,473..63249879

0

chr8:14,696,759-14,702,931

8p22

6173

11.98%

SGCZ (−)

0

1.73

1.35

2.23

2.10E-05

0.024

chr8:14,697,130..14719288

0

chr8:14,702,931-14,710,309

8p22

7379

12.16%

SGCZ (−)

0

1.72

1.33

2.21

2.65E-05

0.030

chr8:14,697,130..14719288

0

chr8:14,720,385-14,737,759

8p22

17,375

5.62%

CTD-2023 J5.1 (−)

0

2.11

1.53

2.89

4.04E-06

0.005

chr8:14,680,345..14849094

0

chr9:40,824,400-40,839,148

9p13.1

14,749

11.05%

ZNF658 (−)

0

1.83

1.37

2.44

3.96E-05

0.045

chr9:40,832,700..41365793

0

chr9:40,857,839-40,876,494

9p13.1

18,656

13.54%

BX664608.1 (+)

44,448

1.72

1.33

2.23

3.88E-05

0.044

chr9:40,832,700..41365793

0

chr9:40,876,494-40,895,281

9p13.1

18,788

13.36%

BX664608.1 (+)

63,103

1.74

1.34

2.25

3.40E-05

0.039

chr9:40,832,700..41365793

0

chr11:55,900,420-55,952,826

11q12.1

52,407

11.79%

OR5J2 (+)

0

1.73

1.34

2.24

3.10E-05

0.035

chr11:55,962,241..55976332

9415

chr11:55,952,826-55,965,828

11q12.1

13,003

11.29%

OR8V1P (−)

0

1.75

1.34

2.26

2.84E-05

0.032

chr11:55,962,241..55976332

0

chr15:23,938,636-23,943,758

15q11.2

5123

7.46%

NDN (−)

6185

1.95

1.42

2.67

3.73E-05

0.042

chr15:23,973,556..23974955

29,798

chr15:29,061,004-29,089,826

15q13.1

28,823

21.10%

GOLGA6L7P (−)

0

1.71

1.32

2.21

3.87E-05

0.044

chr15:29,066,490..29069430

0

chr15:29,089,826-29,154,407

15q13.1

64,582

14.14%

APBA2 (+)

0

1.80

1.36

2.39

3.64E-05

0.041

chr15:29,093,623..29096097

0

  1. aHazard Ratio if genomic deletion is present; Cox regression model includes genomic segment, gender, age, UACR - all dichotomized variables. The linc RNA regions are shown in bold font. b genomic segments with “Distance to nearest gene” >0 indicates that the segment doesn’t cover the gene, but it is close to that gene. c genomic segments with “Distance to nearest reported CNV” = 0 indicates that the identified CNV overlaps with known CNV repoted in the DGV database