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Table 1 Association of HMIP-2 variants with fetal-hemoglobin levels (ln[HbF%]) in Tanzanian patients with SCA

From: Genetic association of fetal-hemoglobin levels in individuals with sickle cell disease in Tanzania maps to conserved regulatory elements within the MYB core enhancer

Marker

Sub-locus

Chr 6 position

allele change

MAF

β

P

β*

P*

β**

P**

β***

P***

rs9376090

 

135,411,228

T → C

0.01

0.78

2.02x 10−4

0.17

0.52

0.51

0.02

−0.09

0.71

rs41294858

 

135,412,636

T → C

0.18

−0.16

3.74x 10−4

−0.14

1.28x 10−3

−0.13

3.35x 10−3

−0.12

6.07x 10−3

rs55731938

 

135,414,850

G → A

0.21

−0.16

1.65x 10−4

−0.15

4.85x 10−4

−0.13

1.79x 10−3

−0.13

2.68x 10−3

rs7745098

 

135,415,004

C → T

0.11

0.15

6.84x 10−3

0.15

5.04X 10−3

0.17

1.73x 10−3

0.17

1.68x 10−3

rs76267242

 

135,417,460

G → T

0.19

−0.16

1.87x 10−4

−0.15

7.52x 10−4

−0.14

1.78x 10−3

−0.13

3.58x 10−3

rs66650371

HMIP-2A

135,418,635

I → D

0.02

0.69

4.06 x 10−8

  

0.59

3.94x 10−6

  

rs9399137

HMIP-2A

135,419,018

T → C

0.02

0.63

3.65 x 10−7

0.14

0.6

0.54

1.87x 10−5

0.13

0.61

rs11321816

 

135,419,038

I → D

0.14

0.12

1.36x 10−2

0.05

0.36

0.12

0.02

0.06

0.26

rs35786788

HMIP-2A

135,419,042

G → A

0.02

0.69

5.07 x 10−8

0.35

0.19

0.61

2.44x 10−6

0.37

0.16

rs1074849

 

135,423,412

G → A

0.13

−0.19

3.09x 10−4

−0.18

5.22x 10−4

−0.17

1.11x 10−3

−0.16

1.37x 10−3

rs4895441

HMIP-2B

135,426,573

A → G

0.05

0.30

1.53x 10−4

0.23

4.06x 10−3

0.13

0.16

0.09

0.35

rs9389269

HMIP-2B

135,427,159

T → C

0.03

0.48

1.11x 10−6

0.37

2.76x 10−4

0.27

0.04

0.16

0.22

rs9402686

HMIP-2B

135,427,817

G → A

0.03

0.49

1.57x 10−6

0.36

6.51x 10−4

0.27

0.04

0.14

0.28

rs1411919

 

135,432,061

A → G

0.34

−0.10

8.67x 10−3

−0.09

0.01

−0.06

0.12

−0.06

0.11

rs9494145

HMIP-2B

135,432,552

T → C

0.05

0.38

4.97 x 10−7

0.31

3.45x 10−5

    

rs2223385

 

135,435,171

G → A

0.39

−0.11

1.74x 10−3

−0.11

2.77x 10−3

−0.08

0.04

−0.08

0.04

rs1320963

 

135,443,212

A → G

0.33

0.09

1.44x 10−2

0.07

0.05

0.03

0.44

0.02

0.54

rs1569534

 

135,451,580

C → T

0.15

−0.12

1.25x 10−2

−0.11

0.02

−0.10

0.04

−0.09

0.06

rs6929404

 

135,454,027

C → A

0.49

0.11

2.35x 10−3

0.09

6.64x 10−3

0.06

0.08

0.06

0.09

  1. linear regression analysis: *conditioned for rs66650371, **conditioned on rs9494145, ***conditioned on rs66650371and rs9494145. (Residual association extends upstream of HMIP-2 and overlaps with the previously reported (Thein et al., PNAS 2007) HMIP-1 signal.).
  2. The chromosomal position is given in hg19 coordinates, derived using UCSC Genome Browser version February 2009.
  3. MAF: Minor allele frequency of the patient cohort; I: inserted allele, D: deleted allele (Δ ‘TAY’). ß, the un-standardized regression co-efficient is given as a measure of the effect of the allele change on ln[%HbF].
  4. Shown are all directly genotyped markers with nominally significant association at p < 0.01.