Table 1 BCC susceptibility novel loci that replicated at P < 0.05 in 23andMe cohort

From: A multi-phenotype analysis reveals 19 susceptibility loci for basal cell carcinoma and 15 for squamous cell carcinoma

rsID

Locus

CHR

BP

EA

NEA

EAF

log (OR)

SE

P value

Nearest gene(s)

eQTL gene (skin)

eQTL gene P value

rs12142181

2

1

41,912,985

T

C

0.08

−0.092

0.015

2.86E-09

EDN2 (−31kb) |FOXO6 ( + 63 kb)

EDN2**

6.26E-05

rs2369633

7

1

205,181,062

C

T

0.10

−0.100

0.015

9.81E-12

DSTYK ( + 0.33 kb)

CNTN2

4.96E-06

rs2111485

13

2

163,110,536

G

A

0.40

−0.052

0.009

3.46E-09

FAP ( + 10 kb) |IFIH1 (−13 kb)

–

–

rs2373232

16

3

46,444,383

A

G

0.32

−0.050

0.009

4.77E-08

CCRL2 (−4 kb) |CCR5 ( + 26 kb)

CCR2/CCR5

8.61E-6/7.88E-9

rs9878566

19

3

156,493,213

T

C

0.48

0.048

0.009

2.36E-08

LINC00886 (0)

LINC00886

1.56E-24

rs6889986

24

5

90,207,399

A

G

0.44

−0.054

0.009

5.44E-10

GPR98 (0)

–

–

rs706779

47

10

6,098,824

C

T

0.48

0.058

0.009

1.43E-11

IL2RA (0)

FHIT (eQTL Gen)

8.16E-07

rs7098111

51

10

119,573,178

T

C

0.15

−0.080

0.012

6.19E-12

RAB11FIP2 (−191 kb)

–

–

rs10766301

52

11

16,217,413

T

C

0.38

0.054

0.009

2.93E-10

SOX6 (0)

–

6.15E-11

rs174570

53

11

61,597,212

T

C

0.16

−0.081

0.013

2.67E-10

FADS2 (0) |FADS1 ( + 12 kb)

–

–

rs2924552

56

11

68,889,367

T

C

0.41

0.061

0.009

3.50E-12

TPCN2 ( + 31 kb)

TPCN2 (eQTL Gen)

2.18E-5/8.94E-157

rs4409785

58

11

95,311,422

C

T

0.19

−0.073

0.011

9.51E-11

FAM76B (−190 kb)

SESN3 (eQTL Gen)

5.37E-62

rs73008229

59

11

108,187,689

A

G

0.16

−0.071

0.012

5.40E-09

ATM (0)

C11orf65

3.18E-05

rs10876864

61

12

56,401,085

A

G

0.41

0.055

0.009

2.56E-10

SUOX ( + 1.78 kb) |IKZF4 (−13 kb)

RPS26/IKZF4/SUOX

3.92E-251/9.86e-9/

3.97e-54

rs17425489

62

12

89,015,138

A

G

0.09

−0.091

0.015

4.54E-10

KITLG ( + 40 kb)

–

 

rs10774625

64

12

111,910,219

G

A

0.48

0.053

0.009

4.03E-10

ATXN2 (0)

ALDH2 (blood)

1.58E-08

rs11059675

65

12

122,668,326

A

G

0.44

−0.049

0.009

1.21E-08

LRRC43 (0) |IL31( + 9 kb)

LRRC43

6.92E-06

rs7301141

66

12

133,138,503

G

A

0.46

0.052

0.009

6.21E-09

FBRSL1 (0)

P2RX2

4.76E-06

rs1136165

69

14

103,988,180

T

G

0.38

0.054

0.009

1.11E-09

CKB (0)

CKB/MARK3

1.88E-22/3.15E-31

  1. Genes are formatted in italics.
  2. CHR chromosome, BP base pair position, EA effect allele, NEA non-effect allele, EAF- effect allele frequency, OR odds ratio (two-sided test), SE standard error, P P value after multiple correction test for a million tests (0.05/1,000,000), eQTL expression quantitative trait loci.
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