Table 1 Previously unreported genome-wide significant loci from meta-analysis of UKB and GERA SNPs for each cancer site.

From: Pan-cancer study detects genetic risk variants and shared genetic basis in two large cohorts

Cancer site

SNP

Chromosome

Position

Gene

REF/ALTa

MAF UKB

MAF GERA

OR UKB

OR GERA

OR Meta

Meta P

Bladder

rs76088467b,c

6

21795787

CASC15

G/A

0.025

0.030

0.67

0.59

0.64

2.34 × 10−8

Breast

rs6752414b,c

2

121425339

Intergenic

T/C

0.077

0.083

0.89

0.87

0.88

1.81 × 10−9

Breast

rs8027730c,d

15

49872585

FAM227B

A/C

0.48

0.48

1.06

1.08

1.06

2.68 × 10−8

Cervix

rs10175462c,d

2

113988492

PAX8

A/G

0.36

0.37

1.16

1.08

1.15

7.71 ×10−14

Cervix

rs2856437b,c

6

32157364

PBX2

A/G

0.063

0.047

0.76

0.88

0.77

1.24 × 10−15

Colon

rs71518872c,d

8

103561978

Upstream of ODF1

G/C

0.015

0.017

0.65

0.61

0.64

1.27 × 10−8

Colon

rs8114643d

20

7833046

Intergenic

G/A

0.14

0.15

0.83

0.84

0.83

2.10 × 10−9

Esophagus/Stomach

rs75460256b,c

2

106687838

C2orf40

G/A

0.024

0.022

0.52

0.67

0.53

1.04 × 10−8

Kidney

rs112248293c,d

15

61500352

RORA

A/G

0.024

0.025

0.53

0.62

0.55

3.36 × 10−9

Lung

rs10863899d

1

211666218

5′UTR of RD3

G/A

0.42

0.42

1.23

1.09

1.18

1.91 × 10−8

Lung

rs146099759d

5

12883592

Intergenic

A/G

0.024

0.028

0.69

0.57

0.64

3.50 × 10−8

Lung

rs12543486b,c

8

13012376

DLC1

C/T

0.17

0.16

1.30

1.18

1.26

3.51 × 10−8

Lymphocytic Leukemia

rs114490818d

3

126099101

Intergenic

A/G

0.022

0.011

0.48

0.53

0.48

2.86 × 10−8

Lymphocytic Leukemia

rs61965473c,d

13

95571786

Intergenic

T/C

0.023

0.023

0.52

0.44

0.49

3.95 × 10−8

Lymphocytic Leukemia

rs78378222b,c

17

7571752

3′UTR of TP53

G/T

0.012

0.014

0.44

0.34

0.40

1.89 × 10−9

Melanoma

rs9818780c,d

3

156492758

Intergenic

C/T

0.49

0.48

0.92

0.89

0.91

3.16 × 10−8

Melanoma

rs12186662d

5

90356197

ADGRV1

G/A

0.32

0.36

0.90

0.89

0.90

1.09 × 10−8

Melanoma

rs55797833b,c

9

21995044

5′UTR OF CDKN2A

G/T

0.023

0.021

1.71

1.72

1.71

6.71 × 10−12

Melanoma

rs78378222b,c

17

7571752

3′UTR of TP53

G/T

0.012

0.014

0.70

0.63

0.67

1.18 × 10−8

Rectum

rs145503185d

9

23455764

Intergenic

C/T

0.013

0.018

0.57

0.50

0.55

4.36 × 10−8

Thyroid

2:173859846_TA_Td

2

173859846

RAPGEF4

T/TA

0.25

0.26

1.45

1.15

1.36

3.49 × 10−8

  1. MAF minor allele frequency calculated in all controls, OR odds ratio.
  2. a REF is reference allele and ALT allele is effect allele; bold allele is minor allele
  3. b Indicates SNPs in known susceptibility loci for cancer of interest in European ancestry but independent of previously reported variants (LD r2 < 0.1 in Europeans).
  4. c Indicates SNPs in loci previously associated with at least one of the other cancers evaluated in this study in European ancestry.
  5. dIndicates SNPs in loci not previously associated with the cancer of interest in European ancestry.
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