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Table 3 List of SNPs that are known to be associated with different levels of HbF and results of the analysis based on pooled DNA samples.

From: A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples

Number

SNP

Band

Gene

Validated

Distance

D'

BF

P_H

P_L

OR

1

rs1143637

2q13

IL1B

rs12469600

16976

NA

1.39

0.13

0.04

3.08

2

rs31481

5q23.3

IL3

rs40401

724

1.00

2.32

0.48

0.65

0.48

3

rs271158

6q23.2

 

rs271156

641

1.00

22.86

0.53

0.77

0.35

4

rs454877

6q23.2

EYA4

rs211433

475

NA

2.43

0.49

0.32

2.09

5

rs212770

6q23.2

EYA4

rs11154727

4274

NA

1.25

0.12

0.04

3.03

6

rs2295199

6q23.2

 

rs2295199

0

 

0.51

0.83

0.89

0.58

7

rs210948

6q23.2

MYB

rs210798

17242

NA

2.17

0.78

0.90

0.38

8

rs509342

6q23.2

PDE7B

rs560713

23645

0.95

1.47

1.00

0.95

17.80

9

rs2076192

6q23.3

MAP7

rs2076193

44438

0.97

1.30

0.52

0.37

1.88

10

rs997139

6q23.3

MAP7

rs3799419

2100

1.00

1.35

0.06

0.14

0.36

11

rs3778314

6q23.3

MAP7

rs2181096

25746

0.89

57.04

0.61

0.85

0.28

12

rs2237262

6q23.3

MAP3K5

rs3799472

18405

0.98

1.03

0.62

0.76

0.53

13

rs2012700

6q23.3

PEX7

rs2012700

0

0

1.50

0.34

0.50

0.52

14

rs717088

6q23.3

PEX7

rs717088

0

 

0.47

0.37

0.47

0.65

15

rs3799476

6q23.3

PEX7

rs3799479

44021

NA

1.98

0.12

0.25

0.42

16

rs1342645

6q23.3

PEX7

rs1342645

0

 

0.67

0.77

0.86

0.55

17

rs1342641

6q23.3

 

rs1342642

22583

0.06

6.12

0.96

0.84

4.98

18

rs1322393

6q23.3

IL20RA

rs1322394

661

1.00

3.00

0.23

0.40

0.44

19

rs44450

6q23.3

 

rs276568

3229

1.00

47.32

0.37

0.64

0.34

20

rs1349115

8q12.1

TOX

rs1349115

0

 

0.69

0.29

0.41

0.59

21

rs10504269

8q12.1

TOX

rs10504269

0

 

0.61

0.72

0.82

0.58

22

rs6997859

8q12.1

TOX

rs6997859

0

 

0.37

0.23

0.17

1.45

23

rs12155519

8q12.1

TOX

rs12155519

0

 

0.94

0.58

0.44

1.77

24

rs1947178

8q12.1

TOX

rs1947178

0

 

21.86

0.10

0.29

0.28

25

rs746867

8q12.1

TOX

rs746867

0

 

0.29

0.29

0.35

0.76

26

rs389349

8q12.1

TOX

rs389349

0

 

0.42

0.95

0.93

1.43

27

rs851800

8q12.1

TOX

rs396720

23622

0.15

9.20

0.28

0.11

3.24

28

rs380620

8q12.1

TOX

rs2561145

300069

0.58

10.67

0.08

0.24

0.26

29

rs2043190

9q34.11

ASS

rs540140

609

NA

19.56

0.99

0.88

24.90

30

rs7482144

11p15.4

HBG2

rs3813727

20257

NA

2.52

0.17

0.32

0.43

31

rs723623

15q13.3

C15orf16

rs6493688

8825

0.51

1.31

0.93

0.84

2.66

32

rs1867380

15q22.31

AQP9

rs1867380

0

 

0.28

0.82

0.84

0.85

33

rs4489951

15q22.31

MAP2K1

rs4489951

0

 

17.66

0.36

0.60

0.38

34

rs1440372

15q22.31

SMAD6

rs2469141

65753

0.03

2181.00

0.68

0.33

4.24

35

rs8038623

15q22.31

SMAD3

rs6494633

16831

NA

87.23

0.88

0.65

4.09

36

rs2227319

17q21.1

CSF3

rs2071369

1460

1.00

3.42

0.90

0.77

2.88

  1. Column 1: row number; Column 2: SNP ID; Column 3: Cytogenic band; Column 4: Genes tagged by the SNP; Column 5: SNP in the Illumina array that was used to compare the association. If the SNP to be validated was not in the array, we searched for the closest SNP within 100 kb from that to be validated with a positive Bayes Factor; Column 6: distance between the two SNPs; Column 7: Bayes D' between the two SNPs, an NA means that the SNPs originally reported as associated with HbF is not in the HapMap data. Column 8: Bayes Factor; Column 9–10: estimates of allele frequencies in the pools of DNA from patients with high HbF and low HbF; Column 11: Odds ratio. The SNPs 6, 13, 14, 16, 20–26, 32 and 33 are in the array and SNPs 13, 24 and 33 were found associated with different levels of HbF. Highlighted in bold are the associations confirmed by our analysis.