Table 1 Concordant SNPs recovered from TCGA and AGS data, and associated genes

rs2736100⁺

5

TERT

5p15.33

SLC6A18

CLPTM1L

NA

5.30E-13

2.66E-04

7.38E-09

rs1412829*⁺

9

CDKN2A/B

9p21.3

LOC100130239

LOC729983

CDKN2A(1.0);

CDKN2B(1.0);

C9orf53(0.87)

3.40E-08

3.26E-03

1.27E-03

rs2157719

9

CDKN2A/B

9p21.3

LOC100130239

LOC729983

CDKN2A(0.97);

CDKN2B(0.97);

C9orf53(0.93);

RP11-145E5.4(0.97);

LOC100130239(0.97)

6.10E-08

8.00E-03

5.40E-03

rs1063192⁺

9

CDKN2A/B

9p21.3

CDKN2A

LOC100130239

CDKN2A(0.97);

CDKN2B(0.97);

C9orf53(0.93);

RP11-145E5.4(0.97);

LOC100130239(0.97)

9.20E-08

8.31E-03

7.95E-03

rs4977756⁺

9

CDKN2A/B

9p21.3

LOC100130239

LOC729983

CDKN2A(0.97);

CDKN2B(0.97);

C9orf53(0.93);

RP11-145E5.4(0.97);

LOC100130239(0.97)

4.20E-07

1.12E-02

3.90E-02

rs7530361

1

SLC35A3

1p21.2

LOC730081

HIAT1

SLC35A3(1.0);

CCDC76(0.95);

HIAT1(1.0);

LRRC39(0.95);

SASS6(1.0);

BRI3P1(0.95);

LOC730081(1.0)

6.50E-07

2.19E-06

4.29E-05

rs501700

1

HIAT1

1p21.2

SLC35A3

SASS6

DBT(0.95);

RTCD1(0.89);

SLC35A3(1.0);

CCDC76(0.95);

HIAT1(1.0);

LRRC39(0.94);

SASS6(1.0);

BRI3P1(0.94);

LOC730081(1.0)

7.10E-07

5.99E-06

9.72E-05

rs1920116

3

LRRC31

3q26.2

LRRIQ4

KRT18P43

MYNN(0.89);

LRRC31(1);

ARPM1(0.85);

KRT18P43(1)

LRRC34(1)

1.40E-06

2.88E-03

2.81E-02

rs506044

1

SASS6

1p21.2

SASS6

LRRC39

DBT(1.0);

RTCD1(0.89);

SLC35A3(0.95);

CCDC76(1.0);

HIAT1(1.0);

LRRC39(1.0);

SASS6(1.0);

BRI3P1(0.95);

LOC730081(0.94)

2.10E-06

2.45E-06

1.57E-04

rs640030

1

SASS6

1p21.2

HIAT1

CCDC76

DBT(1.0);

RTCD1(0.89);

SLC35A3(0.95);

CCDC76(1.0);

HIAT1(1.0);

LRRC39(1.0);

SASS6(1.0);

BRI3P1(0.95);

LOC730081(0.94)

2.40E-06

2.57E-06

1.86E-04

rs687513

1

SASS6

1p21.2

SASS6

LRRC39

DBT(0.95);

RTCD1(0.90);

SLC35A3(0.94);

CCDC76(1.0);

HIAT1(1.0);

LRRC39(1.0);

SASS6(1.0);

BRI3P1(0.95);

LOC730081(0.90)

2.90E-06

3.91E-06

3.03E-04

rs3779505

7

ITGB8

7p15.3

MACC1

LOC100130234

ITGB8(1.0)

3.00E-06

5.67E-04

1.35E-02