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Table 3 SNPs associated disease severity at FDR less than 0.02

From: Genetic modifiers of Hb E/β0 thalassemia identified by a two-stage genome-wide association study

       

Disease Severity

 

HbF%

 

SNP

Chr

BP

Gene

Min

Maj

MAF

OR

P

Bonf

FDR

Beta

SE

P

Var

rs483850

1

203478366

FAIM3

T

A

0.45

0.65

9.7E-04

7.3E-01

0.01

0.05

.05

0.10

.52

rs934956

2

104555647

Intergenic

T

C

0.17

1.93

5.6E-04

4.2E-01

0.01

0.00

.05

0.97

.40

rs370898

3

21442705

ZNF659

G

T

0.05

0.37

1.4E-03

1

0.01

0.01

.05

0.93

.32

rs903047

3

132234707

NEK11

T

C

0.35

1.58

1.5E-03

1

0.01

-0.03

.05

0.44

.30

rs6443662

3

180834067

Intergenic

C

T

0.29

0.58

3.8E-04

2.8E-01

0.005

0.02

.05

0.57

.30

rs950310

4

9519119

SLC2A9

A

T

0.17

2.03

3.5E-04

2.6E-01

0.005

-0.08

.05

0.18

.29

rs258824

5

142577483

ARHGAP26

A

G

0.39

1.58

1.1E-03

8.3E-01

0.01

-0.06

.05

0.12

.29

rs234915

6

2154576

GMDS

A

C

0.21

0.52

1.3E-04

9.5E-02

0.002

0.03

.05

0.45

.27

rs545537

6

117751734

ROS1

A

G

0.17

1.90

8.4E-04

6.3E-01

0.01

0.03

.04

0.59

.27

rs4376364

6

135349178

HBS1L

G

T

0.34

1.70

4.3E-04

3.2E-01

0.01

-0.07

.05

0.10

.27

rs7804867

7

102627708

SLC26A5

A

G

0.28

1.76

3.4E-04

2.6E-01

0.005

-0.03

.05

0.51

.27

rs6972505

7

102657988

SLC26A5

C

G

0.24

2.13

7.6E-06

5.8E-03

0.0001

-0.04

.05

0.35

.27

rs1563408

7

113897140

FOXP2

G

A

0.49

1.63

4.1E-04

3.1E-01

0.01

0.02

.05

0.52

.27

rs766003

9

69709994

c9orf135

G

A

0.16

0.52

2.6E-04

1.9E-01

0.004

0.04

.05

0.37

.25

rs7936823

11

5206792

Intergenic

C

T

0.42

0.23

2.0E-11

1.5E-08

<.0001

0.10

.05

0.04

.25

rs6578588

11

5208867

Intergenic

A

G

0.42

0.21

1.2E-11

9.0E-09

<.0001

0.09

.05

0.07

.24

rs3813727

11

5212511

HBD

T

C

0.42

0.24

8.6E-11

6.5E-08

<.0001

0.10

.05

0.04

.23

rs3759074

11

5214371

Intergenic

T

C

0.41

0.18

3.6E-13 ±

2.7E-10

<.0001

0.10

.05

0.05

.23

rs10837643

11

5214635

Intergenic

A

T

0.43

0.22

5.4E-10

4.1E-07

<.0001

0.14

.05

0.002

.23

rs4320977

11

5214758

Intergenic

T

C

0.42

0.23

1.6E-11

1.2E-08

<.0001

0.10

.05

0.04

.22

rs3759073

11

5214862

Intergenic

A

G

0.42

0.22

2.5E-11

1.9E-08

<.0001

0.09

.05

0.07

.22

rs4402323

11

5215185

Intergenic

G

A

0.42

0.22

4.5E-12

3.4E-09

<.0001

0.10

.05

0.04

.22

rs4910543

11

5215423

Intergenic

C

G

0.42

0.22

5.8E-12

4.4E-09

<.0001

0.10

.05

0.04

.22

rs2105819

11

5216332

Intergenic

C

G

0.42

0.24

4.9E-11

3.7E-08

<.0001

0.11

.05

0.03

.22

rs10128556

11

5220248

HBBP1

A

G

0.42

0.20

3.4E-13

2.6E-10

<.0001

0.10

.05

0.05

.21

rs2071348

11

5220725

HBBP1

C

A

0.41

0.19

4.8E-13

3.6E-10

<.0001

0.09

.05

0.07

.21

rs11036431

11

5222255

HBBP1

T

C

0.43

0.23

6.3E-12

4.8E-09

<.0001

0.08

.05

0.10

.20

rs916111

11

5225911

HBG1

A

T

0.43

0.23

1.7E-11

1.3E-08

<.0001

0.10

.05

0.04

.20

rs2855038

11

5228721

HBG1

A

G

0.43

0.24

4.5E-12

3.4E-09

<.0001

0.10

.05

0.04

.19

rs2855036

11

5229250

HBG2

A

G

0.41

0.20

3.5E-13

2.6E-10

<.0001

0.09

.05

0.08

.19

rs2855126

11

5229721

HBG2

G

C

0.43

0.24

7.0E-12

5.3E-09

<.0001

0.10

.05

0.03

.18

rs2855125

11

5230257

HBG2

A

C

0.43

0.25

1.2E-11

8.8E-09

<.0001

0.12

.04

0.01

.18

rs2236794

11

5230843

HBG2

G

A

0.42

0.24

2.5E-11

1.9E-08

<.0001

0.09

.05

0.07

.17

rs2070972

11

5231293

HBG2

T

G

0.43

0.24

3.6E-12

2.7E-09

<.0001

0.10

.03

0.04

.16

rs2187608

11

5231423

HBG2

G

C

0.41

0.20

7.0E-13

5.3E-10

<.0001

0.09

.04

0.06

.16

rs2070973

11

5231985

HBG2

A

G

0.44

0.23

5.6E-12

4.2E-09

<.0001

0.09

.05

0.06

.16

rs7482144 (XmnI)

11

5232745

HBG2

T

C

0.42

0.20

3.7E-13

2.8E-10

<.0001

0.07

.05

0.17

.15

rs2011051

11

5233395

HBG2

C

A

0.43

0.24

1.2E-11

9.1E-09

<.0001

0.09

.05

0.07

.15

rs2855123

11

5233652

HBG2

T

A

0.44

0.24

4.9E-11

3.7E-08

<.0001

0.07

.05

0.14

.14

rs2855121

11

5233869

HBG2

A

G

0.41

0.20

2.2E-12

1.7E-09

<.0001

0.08

.05

0.12

.12

rs10160820

11

5239027

Intergenic

G

T

0.42

0.19

4.7E-13

3.6E-10

<.0001

0.09

.05

0.09

.12

rs7480802

11

5239080

Intergenic

A

G

0.43

0.24

2.1E-11

1.6E-08

<.0001

0.09

.05

0.07

.11

rs10160747

11

5240751

Intergenic

A

G

0.42

0.20

1.5E-12

1.2E-09

<.0001

0.09

.06

0.08

.11

rs10837707

11

5243234

HBE1

A

G

0.43

0.22

1.4E-12

1.0E-09

<.0001

0.09

.05

0.07

.11

rs4910740

11

5243705

HBE1

C

T

0.42

0.21

9.9E-13

7.5E-10

<.0001

0.10

.05

0.06

.11

bg200 *

11

5245549

HBE1

T

G

0.41

0.18

2.6E-13

2.0E-10

<.0001

0.10

.04

0.07

.10

rs3834466

11

5247976

HBE1

C

A

0.42

0.23

1.7E-11

1.2E-08

<.0001

0.07

.05

0.13

.10

rs3759070

11

5248038

HBE1

C

G

0.41

0.21

1.5E-12

1.1E-09

<.0001

0.08

.04

0.09

.08

rs3759069

11

5248240

HBE1

T

C

0.43

0.23

3.1E-12

2.4E-09

<.0001

0.09

.06

0.06

.08

rs11036562

11

5250549

HBE1

G

T

0.48

0.38

2.7E-08

2.0E-05

<.0001

0.07

.05

0.12

.08

rs11036634

11

5265154

Intergenic

A

G

0.50

2.34

1.4E-06

1.0E-03

<.0001

-0.02

.06

0.65

.07

bg12 *

11

5266933

Intergenic

G

T

0.49

2.31

6.8E-07

5.1E-04

<.0001

-0.06

.05

0.20

.06

rs11036639

11

5267001

Intergenic

C

T

0.46

0.34

6.0E-09

4.5E-06

<.0001

0.06

.04

0.21

.06

rs11036641

11

5267496

Intergenic

A

T

0.49

2.26

2.6E-06

2.0E-03

<.0001

-0.06

.04

0.21

.06

rs11036644

11

5268836

Intergenic

C

T

0.49

2.26

1.5E-06

1.2E-03

<.0001

-0.06

.05

0.18

.06

rs4601817

11

5268977

Intergenic

G

A

0.49

2.25

1.8E-06

1.4E-03

<.0001

-0.07

.05

0.17

.06

bg7 *

11

5270798

Intergenic

G

A

0.46

0.40

2.4E-07

1.8E-04

<.0001

0.05

.04

0.26

.06

rs7933082

11

5273186

Intergenic

C

G

0.48

0.47

1.5E-05

1.2E-02

0.0002

0.05

.04

0.36

.05

rs3888708

11

5274839

Intergenic

T

G

0.50

1.98

5.9E-05

4.5E-02

0.0009

-0.03

.04

0.47

.05

rs6578598

11

5275670

Intergenic

T

C

0.48

0.47

1.1E-05

8.4E-03

0.0002

0.04

.05

0.41

.05

rs10837774

11

5279964

OR51B4

A

G

0.45

0.38

7.3E-08

5.5E-05

<.0001

0.05

.04

0.32

.04

rs3886223

11

5300323

OR51B2

T

G

0.42

0.33

3.7E-11 ±

2.8E-08

<.0001

-0.01

.04

0.83

.04

rs2030090

11

5430669

OR51I2

G

A

0.22

1.81

1.5E-03

1

0.01

0.04

.05

0.46

.04

rs449937

11

5446921

OR51A10P

C

T

0.16

2.08

5.2E-04 ±

3.9E-01

0.01

-0.03

.05

0.64

.03

rs366257

11

5447119

OR51A10P

G

A

0.16

2.21

2.3E-04 ±

1.7E-01

0.003

-0.03

.04

0.58

.03

rs446541

11

5448876

OR51A10P

A

T

0.26

0.48

2.5E-05

1.9E-02

0.0004

0.002

.07

0.96

.03

rs678343

11

64728207

CAPN1

G

C

0.37

1.63

7.1E-04 ±

5.3E-01

0.01

0.04

.04

0.26

.03

rs593753

11

72369088

FCHSD2

T

C

0.29

0.60

6.5E-04 ±

4.9E-01

0.01

0.05

.04

0.21

.02

rs638135

11

85863336

ME3

A

G

0.23

0.59

1.1E-03 ±

8.3E-01

0.01

0.04

.06

0.32

.02

rs632538

11

85869341

ME3

G

A

0.25

0.60

1.5E-03 ±

1

0.01

0.04

.06

0.35

.02

rs2580874

12

8650077

AICDA

G

A

0.20

0.54

4.5E-04

3.4E-01

0.01

0.09

.05

0.04

.02

rs1045411

13

29931232

HMGB1

A

G

0.29

0.58

3.9E-04

2.9E-01

0.005

0.02

.05

0.70

.01

rs886599

14

70244197

Intergenic

A

G

0.10

2.70

1.2E-04

9.0E-02

0.002

0.04

.08

0.64

.01

rs1160027

17

51173101

Intergenic

T

G

0.20

0.56

8.5E-04

6.4E-01

0.01

-0.01

.06

0.79

.01

rs953695

18

59541550

SERPINB11

T

G

0.21

1.83

7.6E-04

5.8E-01

0.01

-0.03

.04

0.63

.01

rs243341

19

4356106

CHAF1A

T

C

0.41

1.59

1.5E-03

1

0.01

-0.04

.04

0.33

.00

rs379327

19

61061978

NLRP4

A

G

0.15

1.97

7.8E-04

5.9E-01

0.01

-0.07

.04

0.26

.00

rs639763

20

33325318

MMP24

T

C

0.30

0.57

3.9E-04

2.9E-01

0.005

-0.04

.07

0.35

.00

rs6625978

X

71201690

PIN4

C

A

0.06

3.35

1.3E-03

1

0.01

-0.001

.04

1.00

.00

  1. BP = location of SNP in base pairs in NCBI build 36
  2. Min = Minor allele
  3. Maj = Major allele
  4. Beta = Absolute change in HbF% on the log scale per copy of the minor allele
  5. SE = Standard error of the Beta estimate
  6. Bonf = Bonferroni adjusted P --value
  7. FDR = false discovery rate
  8. MAF = minor allele frequency
  9. * = SNP not in NCBI database
  10. ± = Chromosome 11 SNPs associated with disease severity at P < 0.05 after adjustment for Xmn1
  11. SNPs significantly associated with disease severity after Bonferroni correction are in bold
  12. P-values for SNPs associated with HbF% at P ≤ 0.05 in the mild disease group are in bold
  13. SNPs in italics were previously shown to be associated with disease severity in this sample by Ma et al. 2007 [19]
  14. Var = Percent of the variation in log transformed HbF% explained by each SNP