Table 1 Summary information for novel independent TGCT susceptibility loci.

From: Identification of 22 susceptibility loci associated with testicular germ cell tumors

Label

Cytoband

rsID

Location (hg19)

A1/A2

A1

frequency

OR

CI

P

Number of genes in region

Adjudicated implicated gene(s)*

Location of signal

a

1p11.1

rs351418

212449403

T/C

0.38

1.11

(1.07, 1.16)

2.85 × 10−8

2

PPP2R5A, PACC1

Proximal, distal

b

2q13

rs6708784

111927379

G/A

0.50

1.11

(1.07, 1.15)

3.91 × 10−8

2

BCL2L11

Distal

c

5p15.33

rs7734992

1280128

T/C

0.60

1.32

(1.26, 1.37)

5.17 × 10−40

1

TERT*

Intronic

d

6p21.32

rs9469079

32032421

T/C

0.13

1.18

(1.11, 1.25)

3.93 × 10−9

1

TNXB

Intronic

e

6p21.32

rs141079110

33533625

A/G

0.75

1.23

(1.18, 1.29)

9.39 × 10−22

1

BAK1*

Distal

f

8q24.12

rs9987332

120933963

A/G

0.44

1.12

(1.08, 1.16)

2.34 × 10−9

1

DEPTOR

Intronic

g

9p24.3

rs10976519

779507

G/T

0.42

1.16

(1.12, 1.20)

1.04 × 10−15

0

[DMRT1]*

Proximal

h

9q33.3

rs10818964

127190340

G/A

0.67

1.13

(1.09, 1.18)

7.92 × 10−10

0

Undetermined

–

i

9q34.3

rs28393706

140073294

T/C

0.75

1.18

(1.13, 1.23)

1.20 × 10−11

3

SSNA1, ANAPC2, TPRN

Intronic, proximal, distal

j

10p14

rs7912968

7534248

C/G

0.38

1.11

(1.07, 1.16)

1.50 × 10−8

0

Undetermined

–

k

11p14.1

rs7927974

30351223

G/A

0.29

1.12

(1.08, 1.17)

4.03 × 10−8

2

ARL14EP, MPPED2

Intronic, distal

l

12p13.33

rs2887532

1051495

C/T

0.82

1.17

(1.11, 1.23)

6.23 × 10−10

1

RAD52

Intronic

m

12q13.13

rs12830125

51301431

C/G

0.34

1.14

(1.09, 1.19)

2.18 × 10−9

2

Undetermined

–

n

12q13.2

rs35969688

53793209

A/G

0.18

1.17

(1.12, 1.23)

4.32 × 10−11

2

SP1, AMRH2

Intronic, proximal

o

17q25.3

rs55779573

76691564

C/T

0.53

1.13

(1.09, 1.17)

1.08 × 10−10

2

CYTH1, USP36

Intronic, distal

p

18p11.32

rs2847334

692095

G/A

0.57

1.11

(1.07, 1.16)

4.16 × 10−8

1

ENOSF1

Intronic

q

19q12

rs8104804

28356614

C/T

0.19

1.17

(1.12, 1.23)

1.38 × 10−10

1

LOC101927151

Intronic

r

20q13.2

rs6068588

52197366

A/C

0.12

1.18

(1.11, 1.25)

1.32 × 10−8

2

ZNF217

Intronic

s

Xp22.11

rs72620486

24384181

T/C

0.15

1.14

(1.09, 1.19)

2.74 × 10−9

2

SUPT20HL1, PDK3

5’ UTR, proximal

t

Xq12

rs2335864

66489986

G/A

0.20

1.15

(1.10, 1.20)

3.39 × 10−11

0

[AR]

Proximal

u

Xq22.1

rs2360670

100432681

A/T

0.54

1.14

(1.10, 1.17)

2.08 × 10−15

2

[CENPI, DPR2]

Distal, proximal

v

Xq28

rs4898474

153535143

C/T

0.31

1.18

(1.14, 1.22)

3.60 × 10−19

2

TKTL1*

Intronic, proximal

  1. Detailed information on the meta-analysis and evaluation of the 22 top signals can be found in Supplementary Data 1, 5, 8 and Supplementary Table 8. Label refers to letter designation in Fig. 1a, b. Novel independent signals in a previously identified gene are indicated with an asterisk (*). Number of genes in the region is defined by r2 > 0.80 of the top signal. Associations were tested using a two-sided Wald test on the logistic regression coefficient with an alpha level of 5 × 10−8 to account for multiple comparisons. Genes evaluated as highly likely to be the target genes are indicated in bold font, and those evaluated as moderately likely are not bold. Genes listed in [brackets] indicate those evaluated as low likelihood to be the target gene. However, one is a well-established TGCT susceptibility gene (DMRT1) and the others are located on the X chromosome for which some data is lacking for complete target gene evaluation.
  2. A1 risk allele, OR odds ratio, CI confidence interval, P P-value for fixed-effects meta-analysis.
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