Table 3

Fifteen coding variants with functionally characterized SNPs crossing the threshold (P < 10-6) for association with C3 scores

Gene

Marker

Chromosome

Chromosome position

Amino acid position

Amino acid change

Correlation/trend P

Correlation/trend R

Minor allele

AJ frequency

CEU frequency

TSI frequency

GIH frequency


CFTR

rs213950

7

116986769

1408

V | M

2.29E-08

-0.155

A

0.287

0.487

0.347

0.489

ABCB1

rs1045642

7

86976581

3435

4.95E-11

-0.183

A

0.367

0.571

0.466

0.597

GSTP1

rs1138272

11

67110155

341

A | V

4.74E-08

-0.152

T

0.046

0.097

0.062

0.091

MTHFR

rs1801133

1

11778965

665

A | V

6.70E-10

0.172

A

0.435

0.31

0.46

0.17

PPARG

rs1801282

3

12368125

34

P | A

3.21E-09

-0.165

G

0.058

0.097

0.074

0.091

MC1R

rs1805005

16

88513345

178

V | L

4.80E-16

0.227

T

0.266

0.006

0.159

0.006

PLAU

rs2227564

10

75343107

422

L | P

4.82E-08

-0.152

T

0.107

0.239

0.188

0.369

PER1

rs2253820

17

7988894

2361

1.22E-11

0.188

T

0.378

0.185

0.165

0.222

ALF1

rs2269475

6

31691910

43

R | W

2.70E-08

-0.155

T

0.039

0.159

0.091

0.097

HLA-DRA

rs3135391

6

32518965

402

8.47E-10

-0.171

A

0.034

0.19

0.08

0.017

SH2B3

rs3184504

12

110368991

784

W | R

1.36E-10

-0.179

C

0.365

0.555

0.472

0.869

DKK3

rs3206824

11

11942637

1003

R | G

1.44E-08

-0.158

T

0.128

0.243

0.165

0.148

LCT

rs3754689

2

136307216

655

V | I

1.05E-09

0.17

T

0.466

0.102

0.402

0.29

PPARGC1A

rs3755863

4

23424620

1584

4.99E-08

0.052

T

0.473

0.412

0.511

0.398

NOD2

rs2067085

16

49291359

639

9.54E-08

0.151

G

0.536

0.381

0.455

0.207


AJ, Ashkenazi Jew; CEU, Northern Europe; GIH, Gujarat India; TSI, Southern Europe Tuscan.

Guha et al. Genome Biology 2012 13:R2   doi:10.1186/gb-2012-13-1-r2

Open Data