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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