Table 2 Summary of the variants newly satisfying the genome-wide significance threshold from the single/all cancer GWAS/meta-analysis

From: Pan-cancer and cross-population genome-wide association studies dissect shared genetic backgrounds underlying carcinogenesis

Cancer type

Cohort

Chr:Position

rsID

REF/ALT

Nearest gene

Functional annotation

Discovery

Replication

BioBank Japan 1 (BBJ1)

UK Biobank (UKB)

Cross-population

BBJ2

BBJ1 + BBJ2

BBJ1 + UKB + BBJ2

EAF

OR

P

EAF

OR

P

OR

P

OR

P

OR

P

OR

P

Single cancer GWAS/meta-analysis

Breast

BBJ/UKB

1:17719005

rs2800691

C/T

PADI6

Intron

0.35

0.93

0.0013

0.27

0.94

7.5 × 10−6

0.94

3.6 × 10−8

0.97

0.20

0.95

0.0010

0.94

3.1 × 10−8

Colorectal

UKB

6:158652195

rs143926630

GA/G

TULP4

Intergenic

–

–

–

0.26

1.12

1.3 × 10−8

–

–

–

–

–

–

–

–

Hepatocellular

BBJ

12:113117897

rs77753011

G/T

RPH3A

Intron

0.08

0.77

8.1 × 10−7

–

–

–

–

–

0.78

1.4 × 10−9

0.78

5.5 × 10−15

–

–

Lung

BBJ/UKB

6:7563232

rs2076295

T/G

DSP

Intron

0.49

1.12

1.4 × 10−6

0.45

1.07

0.0018

1.10

2.6 × 10−8

1.10

1.7 × 10−4

1.11

1.1 × 10−9

1.10

1.8 × 10−11

NHL

UKB

19:19269254

rs370149412

TAA/T

MEF2B

Intron

–

–

–

0.46

1.20

4.7 × 10−8

–

–

–

–

–

–

–

–

All-cancer meta-analysis

All-cancer

BBJ

1:222841614

rs36079339

G/A

AIDA

UTR3

0.54

0.95

6.9 × 10−7

0.72

1.00

0.90

0.98

6.1 × 10−4

0.96

1.0 × 10−4

0.96

3.9 × 10−10

–

–

All-cancer

BBJ

3:185508591

rs11927381

T/C

IGF2BP2

Intron

0.34

0.95

2.4 × 10−8

0.31

0.99

0.37

0.97

1.9 × 10−5

0.97

4.4 × 10−4

0.96

1.3 × 10−10

–

–

All-cancer

UKB

1:107566689

rs56111229

T/A

PRMT6

Intergenic

0.29

1.00

0.94

0.35

1.05

2.0 × 10−8

1.03

1.3 × 10−5

–

–

–

–

–

–

All-cancer

BBJ/UKB

4:148276400

rs2059904

A/G

EDNRA

Intergenic

0.32

1.05

2.2 × 10−6

0.17

1.02

0.022

1.04

6.9 × 10−7

1.03

0.0041

–

–

1.03

1.2 × 10−8

All-cancer

BBJ/UKB

7:99553167

rs2525548

C/G

AZGP1

Intergenic

0.35

0.96

1.0 × 10−5

0.58

0.97

3.8 × 10−5

0.96

2.5 × 10−9

0.99

0.15

–

–

0.97

5.1 × 10−9

  1. All statistical tests are two-sided and not adjusted for multiple comparisons. P values satisfying the genome-wide significance threshold are shown in bold.
  2. Chr chromosome, REF reference allele, ALT alternative allele, EAF effect allele frequency in the control subjects, OR odds ratio, NHL Non-Hodgkin’s lymphoma.
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