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Table 1 Results of GWAS conducted in All-PD and stratified by Sporadic-PD and Familial-PD

From: Identification of a novel Parkinson’s disease locus via stratified genome-wide association study

CHR Gene

SNP

Base pair position*

Minor/major allele

Allele frequency

Association with PD

Case

Control

All-PD

Sporadic-PD

Familial-PD

All-PD

Sporadic

Familial

 

OR

SE

P

OR

SE

P

OR

SE

P

Known highly significant loci

4 SNCA

rs356220

90641340

T/C

0.440

0.439

0.443

0.364

1.38

0.07

3×10-11

1.37

0.07

1×10-9

1.40

0.11

2×10-5

6 HLA

rs3129882

32409530

G/A

0.459

0.470

0.418

0.395

1.31

0.06

3×10-8

1.38

0.07

5×10-10

1.12

0.09

0.15

17 MAPT

rs199498

44865603

C/T

0.190

0.197

0.162

0.236

0.74

0.05

2×10-6

0.78

0.05

2×10-4

0.59

0.06

8×10-7

New Signals in NGRC

1

rs2338971

101880005

T/C

0.187

0.179

0.213

0.232

0.74

0.04

2×10-7

0.71

0.04

4×10-8

0.86

0.08

0.12

8

rs12681349

4277990

T/C

0.376

0.369

0.403

0.426

0.78

0.04

7×10-7

0.75

0.04

5×10-8

0.88

0.07

0.10

Replication

1

rs2338971

101880005

T/C

0.184

0.182

0.188

0.212

0.82

0.06

5×10-3

0.81

0.07

6×10-3

0.83

0.08

0.03

8

rs12681349

4277990

T/C

0.427

0.420

0.442

0.419

1.02

0.06

0.38

0.99

0.06

0.41

1.09

0.08

0.13

Pooled NGRC and Replication

1

rs2338971

101880005

T/C

0.185

0.181

0.197

0.227

0.76

0.03

5×10-10

0.74

0.04

4×10-10

0.82

0.05

2×10-3

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