Table 3 Top 10 independent SNPs from meta-analysis of progression to Hoehn and Yahr stage 3 or greater

From: Genome-wide determinants of mortality and motor progression in Parkinson’s disease

chr

bp

rsID

effect allele

non-effect allele

effect allele freq

nearest gene

distance to gene (BP)

beta

SE

Hazard Ratio

95% CI

p-value

p-value COJO

1

2315032

rs115217673

A

G

0.016

MORN1

0

1.016

0.172

2.762

1.97-3.87

3.09E−09

3.53E−09

7

97470925

rs145274312

A

G

0.011

ASNS

10504

1.872

0.317

6.503

3.49-12.11

3.49E−09

NA*

4

120566153

rs113120976

T

C

0.013

PDE5A

16172

1.581

0.273

4.859

2.85-8.30

6.95E−09

8.72E−09

2

61742356

rs141421624

G

A

0.017

XPO1

0

0.923

0.167

2.517

1.82-3.49

3.08E−08

3.36E−08

1

231267735

rs74796254

T

C

0.027

LOC149373

52110

0.693

0.131

2.000

1.55-2.58

1.17E−07

1.27E−07

1

247425485

rs72771919

G

A

0.021

VN1R5

5038

0.770

0.146

2.160

1.62-2.88

1.44E−07

1.55E−07

4

186697549

rs75614365

C

G

0.121

SORBS2

0

0.372

0.071

1.450

1.26-1.67

1.94E−07

2.13E−07

1

43105085

rs75140767

G

A

0.028

PPIH

18621

0.715

0.140

2.044

1.55-2.69

3.26E−07

3.49E−07

2

131557187

rs7566590

A

G

0.042

AMER3

31480

0.573

0.112

1.774

1.42-2.21

3.31E−07

3.58E−07

6

11284774

rs148949229

A

G

0.014

NEDD9

0

1.694

0.334

5.441

2.83-10.46

3.78E−07

4.72E−07

15

82198898

rs58698247

C

T

0.024

MEX3B

135221

0.692

0.136

1.997

1.53-2.61

3.94E−07

4.20E−07

  1. Independent SNPs identified with GCTA-COJO. Genome coordinates are in build hg19/GRCh37.
  2. *One SNP, rs145274312, was not included in the COJO analysis as it was not present in the AMP-PD reference dataset. This is likely because the minor allele frequency is close to 1% in the general population (0.97% in gnomAD non-Finnish European population), however in our PD datasets the allele frequency was >1%.
  3. BP base pair, chr chromosome, CI Confidence Interval, freq frequency, GCTA-COJO Genome-wide Complex Trait Analysis conditional and joint analysis, SE Standard Error, SNP Single Nucleotide Polymorphism.
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