Table 2

Pearson's chi-square test for cases versus controls of SNPs and most frequent hgs

rCRS ref.a

MAb

MAFCAc

MAFCOc

CHI2 Exact

P-value

Adjusted P-valued

OR (95% CI)e


3010G > A

G

A

0.24

0.27

0.557

0.455

1

0.85 (0.56-1.29)

3915G > A

G

A

0.02

0.04

0.874

0.350

0.995

0.57 (0.17-1.89)

3992C > T

C

T

0.00

0.01

1.320

0.251

0.979

-

4216T > C

T

C

0.13

0.16

0.939

0.333

0.993

0.77 (0.46-1-30)

4336T > C

T

C

0.04

0.04

0.047

0.828

1

1.11 (0.45-2.72)

4529A > T

A

T

0.01

0.01

0.182

0.669

1

0.64 (0.08-5.13)

4580G > A

G

A

0.06

0.03

1.620

0.203

0.941

1.69 (0.75-3.82)

4769A > G

A

A

0.02

0.02

0.060

0.799

1

1.17 (0.34-4.04)

4793A > C

A

G

0.00

0.01

1.166

0.280

0.987

-

6776T > C

T

C

0.04

0.05

0.577

0.448

1

0.69 (0.27-1.79)

7028C > T

C

C

0.40

0.44

0.683

0.409

0.999

1.16 (0.81-1.67)

10398A > G

A

G

0.15

0.20

2.010

0.156

0.902

0.70 (0.43-1.15)

10400C > T

C

T

0.02

0.01

1.023

0.312

0.991

1.97 (0.52-7.52)

10463T > C

T

C

0.09

0.09

0.001

0.982

1

1.01 (0.53-1.92)

10873T > C

T

C

0.06

0.04

1.609

0.205

0.951

0.61 (0.28-1.32)

12308A > G

A

G

0.19

0.23

1.270

0.260

0.982

0.77 (0.49-1.21)

12705C > T

C

T

0.14

0.08

4.857

0.028

0.315

1.82 (1.06-3.13)

13966A > G

A

G

0.02

0.02

0.001

0.972

1

1.02 (0.29-3.58)

14766C > T

C

T

0.47

0.49

0.242

0.622

1

0.91 (0.64-1.31)

H

-

-

0.40

0.44

0.791

0.374

0.999

0.85 (0.59-1.22)

H1

-

-

0.16

0.19

0.689

0.406

0.999

1.22 (0.76-1.96)

HV

-

-

0.52

0.50

0.121

0.728

1

1.06 (0.75-1.51)

U

-

-

0.19

0.23

1.248

0.264

0.983

1.29 (0.83-2.01)

J

-

-

0.03

0.08

4.411

0.036

0.390

2.61 (1.03-6.61)

T

-

-

0.09

0.08

0.077

0.782

1

0.92 (0.49-1.71)

JT

-

-

0.12

0.16

1.727

0.189

0.941

1.42 (0.84-2.41)


rCRS = revised Cambridge Reference Sequence; MA = minor allele; MAF = minimum allele frequency.

arCRS: allele in the revised Cambridge Reference Sequence (rCRS)[41];

bMA: minor allele;

cMAF: minimum allele frequency computed on cases (MAFCA) and control (MAFCO) individuals;

dAdjusted P-value: adjustment of chi-square P-values was carried out with a permutation-based approach; number of permutations = 20,000;

eOR (95%CI): ORs were computed with the rCRS allele as a reference

Álvarez-Iglesias et al. BMC Medical Genetics 2011 12:50   doi:10.1186/1471-2350-12-50

Open Data