Table 1 Validation of GWAS-identified variants for CLL.

From: Validation and functional characterization of GWAS-identified variants for chronic lymphocytic leukemia: a CRuCIAL study

SNP

Chr.

Nearby gene

Risk allele

CRuCIAL consortium (n = 3105; 1158 CLL cases and 1947 controls)

Previously published GWASb

Meta-analysis

 

OR (95% CI)a

P

OR (95% CI)

P

OR (95% CI)

P

PHet

rs4368253

18

AC107990.1||NFE2L3P1

C

1.30 (1.13–1.49)

2.0E−04

1.18 (1.11–1.26)

8.00E−07

1.20 (1.13–1.27)

5.55E−10

0.212

rs58055674

2

ACOXL

C

1.17 (1.01–1.35)

0.032

1.44 (1.33–1.56)

5.00E−20

1.37 (1.28–1.47)

7.01E−19

0.014

rs1439287

2

ACOXL

T

1.26 (1.11–1.41)

0.0002

1.37 (1.26–1.47)

5.00E−15

1.34 (1.25–1.43)

1.62E−18

0.249

rs7944004

11

ASCL2||C11orf21

T

1.10 (0.97–1.24)

0.12

1.20 (1.13–1.27)

2.00E−10

1.18 (1.12–1.25)

6.44E−10

0.209

rs4987855

18

BCL2

G

1.42 (1.15–1.76)

0.0012

1.47 (1.32–1.61)

3.00E−12

1.46 (1.34–1.60)

1.50E−16

0.773

rs2651823

11

C11orf21|TSPAN32

A

1.09 (0.97–1.23)

0.15

1.18 (1.13–1.25)

5.00E−11

1.17 (1.11–1.22)

9.62E−11

0.228

rs1476569

4

CAMK2D

G

0.97 (0.86–1.10)

0.66

1.18 (1.12–1.25)

6.00E−10

1.14 (1.09–1.20)

2.01E−07

0.004

rs3769825

2

CASP8

T

1.05 (0.93–1.19)

0.40

1.19 (1.12–1.25)

3.00E−09

1.17 (1.11–1.23)

2.12E−09

0.069

rs7558911

2

CFLAR

A

1.02 (0.91–1.16)

0.71

1.18 (1.12–1.24)

5.00E−11

1.16 (1.10–1.21)

1.94E−09

0.030

rs1036935

18

CXXC1

A

1.20 (1.05–1.38)

0.0091

1.15 (1.10–1.21)

3.00E−08

1.16 (1.10–1.21)

3.02E−10

0.564

rs1359742

9

DMRTA1

G

1.18 (1.04–1.32)

0.0078

1.20 (1.12–1.28)

7.00E−09

1.20 (1.13–1.27)

1.98E−09

0.809

rs6546149

2

DTNB

G

1.05 (0.92–1.20)

0.46

1.09 (1.01–1.17)

2.14E−02

1.08 (1.01–1.15)

0.018

0.629

rs9880772

3

EOMES|LINC01980

T

1.27 (1.13–1.43)

5.97E−05

1.19 (1.13–1.25)

2.55E−11

1.20 (1.15–1.26)

7.39E−15

0.319

rs13015798

2

FAM126B

A

0.98 (0.86–1.13)

0.82

1.20 (1.14–1.30)

3.00E−08

1.15 (1.09–1.23)

1.76E−06

0.009

rs6586163

10

FAS

A

1.29 (1.14–1.46)

4.50E−05

1.23 (1.17–1.29)

1.00E−15

1.24 (1.18–1.30)

3.20E−20

0.483

rs2267708

7

GPR37

T

1.22 (1.08–1.37)

0.0012

1.16 (1.10–1.22)

9.00E−09

1.17 (1.12-1.23)

1.04E−10

0.446

rs35923643

11

GRAMD1B

G

1.93 (1.66–2.24)

6.20E−16

1.66 (1.54-1.79)

2.00E−40

1.71 (1.60–1.83)

2.76E−55

0.078

rs2953196

11

GRAMD1B

G

1.29 (1.12–1.49)

6.00E−04

1.30 (1.22–1.38)

5.00E−16

1.30 (1.23–1.37)

1.45E−19

0.922

rs3800461

6

ILRUN

C

1.12 (0.90–1.38)

0.32

1.20 (1.13–1.28)

1.97E−08

1.19 (1.12–1.27)

6.80E−09

0.544

rs9392504

6

IRF4

A

1.46 (1.29–1.64)

1.75E−09

1.33 (1.26–1.40)

1.00E−28

1.35 (1.29–1.42)

3.14E−34

0.163

rs391855

16

IRF8

A

1.20 (1.06–1.36)

0.0031

1.37 (1.28–1.45)

1.00E−22

1.33 (1.26–1.41)

3.94E−24

0.062

rs898518

4

LEF1

A

0.95 (0.84–1.08)

0.41

1.20 (1.14–1.27)

4.00E−10

1.15 (1.10–1.21)

1.16E−08

0.001

rs34676223

1

MDS2

C

1.17 (1.03–1.33)

0.015

1.19 (1.14–1.25)

5.04E−13

1.19 (1.14–1.24)

7.23E−15

0.807

rs57214277

4

MYL12BP2||LINC02363

T

1.06 (0.92–1.23)

0.43

1.13 (1.08–1.18)

3.69E−08

1.12 (1.08–1.17)

6.50E−08

0.409

rs10936599

3

MYNN

C

1.12 (0.96–1.29)

0.14

1.26 (1.17–1.35)

1.74E−09

1.22 (1.16–1.31)

2.11E−10

0.160

rs11715604

3

NCK1

T

0.98 (0.84–1.14)

0.80

NA (NA-NA)

1.97E−08

NA (NA-NA)

NA

NA

rs6489882

12

OAS3

G

1.09 (0.96–1.23)

0.19

1.16 (1.10–1.22)

5.00E−08

1.15 (1.10–1.21)

1.13E−08

0.364

rs140522

22

ODF3B

T

1.17 (1.03–1.32)

0.016

1.15 (1.10–1.20)

2.70E−09

1.15 (1.11–1.20)

1.35E−11

0.797

rs2236256

6

OPRM1||IPCEF1

C

1.20 (1.06–1.35)

0.0037

1.23 (1.15–1.30)

1.50E−10

1.22 (1.16–1.29)

4.49E−13

0.721

rs11637565

15

PCAT29|LOC107984788

G

1.20 (1.06–1.36)

0.0040

1.35 (1.28–1.42)

2.00E−31

1.33 (1.27–1.39)

6.19E−31

0.087

rs17246404

7

POT1

C

1.28 (1.12–1.46)

3.68E−04

1.22 (1.14–1.31)

3.40E−08

1.23 (1.16–1.31)

2.71E−11

0.530

rs2511714

8

POU5F1P2||ODF1

G

1.08 (0.95–1.22)

0.23

1.19 (1.11–1.27)

2.00E−07

1.16 (1.10–1.24)

4.89E−07

0.181

rs11083846

19

PRKD2

A

1.17 (1.01–1.33)

0.030

1.35 (1.22–1.49)

3.96E−09

1.29 (1.19–1.39)

1.24E−09

0.099

rs888096

2

QPCT||RNU6-1116P

A

1.09 (0.97–1.24)

0.16

1.15 (1.09–1.21)

5.00E−08

1.14 (1.09–1.20)

5.37E−08

0.431

rs41271473

1

RHOU

G

0.95 (0.80–1.12)

0.52

1.19 (1.13–1.26)

1.06E−10

1.17 (1.11–1.23)

7.76E−09

0.013

rs73718779

6

SERPINB6

A

0.93 (0.76–1.14)

0.47

1.26 (1.16–1.36)

1.97E−08

1.21 (1.12–1.30)

4.51E−07

0.006

rs12638862

3

TERC

A

1.09 (0.94–1.25)

0.25

1.15 (1.09–1.19)

2.00E−11

1.15 (1.10–1.19)

2.72E−10

0.481

rs7705526

5

TERT

A

1.27 (1.11–1.45)

5.0E−04

1.18 (1.12–1.25)

6.00E−10

1.19 (1.13–1.26)

1.06E−11

0.319

rs61904987

11

TMPRSS5||DRD2

T

1.24 (1.02–1.52)

0.032

1.24 (1.16–1.32)

2.46E−11

1.24 (1.17–1.32)

6.90E−12

1.000

rs926070

6

TSBP1-AS1

A

1.08 (0.95–1.24)

0.24

1.27 (NA–NA)

4.00E−08

NA (NA-NA)

NA

NA

rs7254272

19

ZBTB7A|MAP2K2

A

1.06 (0.91–1.22)

0.46

1.17 (1.10–1.23)

4.67E−08

1.15 (1.10–1.21)

5.93E−08

0.202

  1. OR and 95% CI was not reported in the original study and, therefore, association estimates were not available in the GWAS catalog. In bold in the CRuCIAL cohort, SNPs with P values <0.05. In bold in the meta-analyses, SNPs with a P value <5.5 × 10−8 (gold standard significance threshold for GWAS). Considering the relatively low power of the CRuCIAL cohort, PHet threshold was set to 0.01.
  2. NA not available.
  3. aAssociation estimates calculated according to a log-additive model of inheritance and adjusted for age, sex and country of origin.
  4. bReferences (Pubmed ID) to previously published GWAS are included in the Supplementary Material available on the Blood Cancer Journal website.
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