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Table 4 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 in subjects with higher arsenic exposure (urinary arsenic creatinine ratio > = median value of 192 μg/g of creatinine)

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

CNV genomic coordinates (GRCh37/hg19)

cytoband

length (bps)

Nearest Gene

Distance to Nearest Gene (bps)b

HR (gene) high UACRa

95% CI (gene)

p-value (gene)

Bonferroni p-value (gene) high UACR

interaction p-value high UACR

Nearest reported CNV in DGV database

Distance to Nearest reported CNV (bps)c

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

2q12.1

14,535

RP11-76I14.1 (+)

0

2.05

1.52

2.76

2.41E-06

0.003

0.077

chr2:104,593,605..104760102

35,513

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

2q12.1

10,358

RP11-76I14.1 (+)

0

2.05

1.52

2.76

2.21E-06

0.003

0.075

chr2:104,593,605..104760102

25,156

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

2q12.1

7849

RP11-76I14.1 (+)

0

1.98

1.47

2.67

5.86E-06

0.007

0.103

chr2:104,593,605..104760102

12,334

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

3q12.3

53,118

RNU1-43P (+)

108,357

2.39

1.60

3.57

2.11E-05

0.024

0.348

chr3:102,743,602..102752706

0

chr5:117,349,895-117,357,592

5q23.1

7698

CTD-3179P9.1 (+)

0

2.36

1.57

3.56

3.80E-05

0.043

0.013

chr5:117,280,136..117451273

0

chr5:117,357,592-117,368,561

5q23.1

10,970

CTD-3179P9.1 (+)

0

2.35

1.56

3.53

4.37E-05

0.050

0.016

chr5:117,280,136..117451273

0

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

5q34

8786

CTC-535 M15.2 (+)

0

2.57

1.69

3.89

9.35E-06

0.011

0.224

chr5:164,849,860..164874815

42,367

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

5q34

13,655

CTC-535 M15.2 (+)

0

2.51

1.67

3.78

1.03E-05

0.012

0.214

chr5:164,849,860..164874815

51,152

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

5q34

16,502

CTC-535 M15.2 (+)

0

2.49

1.65

3.75

1.23E-05

0.014

0.223

chr5:164,849,860..164874815

64,806

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

5q34

17,054

CTC-535 M15.2 (+)

0

2.50

1.65

3.78

1.65E-05

0.019

0.287

chr5:164,849,860..164874815

81,307

  1. aHazard Ratio if genomic deletion is present; Cox regression model includes: genomic segment, age, gender, UACR and interaction term “genomic segment x UACR”. Rows representing linc RNA regions are shown in bold font
  2. bgenomic segments with “Distance to nearest gene” >0 indicates that the segment doesn’t cover the gene, but it is close to that gene. cgenomic segments with “Distance to nearest reported CNV” = 0 indicates that the identified CNV overlaps with known CNV repoted in the DGV
  3. Top genomic segments are sorted by chromosome