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Table 2 Characteristics of 39 genetic variants in PD and AD GWAS datasets

From: Parkinson’s disease and Alzheimer’s disease: a Mendelian randomization study

SNP

Chr

Pos

Nearby Genes

EA

NEA

EAFa

PD

AD GWAS

Betab

SE

P value

Betab

SE

P value

rs10797576

1

232,664,611

SIPA1L2

T

C

0.127

0.113

0.014

8.41E-13

0.006

0.022

0.795

rs10906923

10

15,569,598

FAM171A1

A

C

0.461

0.073

0.014

1.35E-8

−0.033

0.017

0.051

rs11060180

12

123,303,586

OGFOD2

A

G

0.748

0.105

0.011

2.05E-20

0.032

0.019

0.081

rs11158026

14

55,348,869

GCH1

C

T

0.490

0.094

0.011

4.30E-16

−0.002

0.017

0.894

rs115185635

3

87,520,857

CHMP2B

C

G

0.012

0.191

0.048

1.22E-4

−0.022

0.058

0.702

rs11724635

4

15,737,101

FAM200B, CD38

A

C

0.408

0.105

0.011

1.22E-19

−0.032

0.016

0.040

rs117896735

10

121,536,327

BAG3

A

G

0.004

0.501

0.057

2.23E-19

0.133

0.086

0.119

rs12456492

18

40,673,380

SYT4

G

A

0.330

0.095

0.012

5.56E-16

0.009

0.017

0.589

rs12497850

3

48,748,989

NCKIPSD, CDC71

T

G

0.731

0.073

0.014

9.16E-9

0.028

0.017

0.088

rs12637471

3

182,762,437

MCCC1

G

A

0.663

0.163

0.015

2.11E-30

0.002

0.019

0.909

rs13294100

9

17,579,690

SH3GL2

G

T

0.457

0.083

0.014

4.84E-13

0.013

0.017

0.453

rs14235

16

31,121,793

ZNF646, KAT8

A

G

0.359

0.077

0.009

5.44E-12

0.041

0.016

0.011

rs1474055

2

169,110,394

STK39

T

C

0.201

0.186

0.018

5.68E-26

0.004

0.024

0.881

rs1555399

14

67,984,370

TMEM229B

T

A

0.607

0.086

0.012

9.61E-11

−0.021

0.016

0.194

rs199347

7

23,293,746

KLHL7, NUPL2, GPNMB

A

G

0.483

0.094

0.011

3.51E-18

−0.033

0.016

0.039

rs2280104

8

22,525,980

SORBS3, PDLIM2, C8orf58, BIN3

T

C

0.265

0.068

0.012

2.53E-8

−0.002

0.016

0.923

rs2414739

15

61,994,134

VPS13C

A

G

0.679

0.094

0.011

3.94E-14

−8.00E-04

0.017

0.964

rs2694528

5

60,273,923

ELOVL7

C

A

0.135

0.140

0.020

4.84E-15

−0.028

0.027

0.305

rs2740594

8

11,707,174

CTSB

A

G

0.893

0.086

0.012

5.91E-12

0.002

0.018

0.926

rs329648

11

133,765,367

MIR4697

T

C

0.465

0.086

0.012

1.11E-13

−0.007

0.018

0.701

rs34043159

2

102,413,116

IL1R2

C

T

0.332

0.077

0.009

5.48E-11

0.006

0.016

0.695

rs34311866

4

951,947

TMEM175,DGKQ

C

T

0.140

0.207

0.014

1.47E-50

0.009

0.021

0.685

rs353116

2

166,133,632

SCN3A

C

T

0.557

0.062

0.011

2.98E-8

0.038

0.016

0.021

rs356182

4

90,626,111

SNCA

G

A

0.404

0.285

0.012

5.21E-123

−0.056

0.017

0.001

rs35749011

1

155,135,036

GBA

A

G

0.005

0.545

0.044

2.59E-35

0.188

0.071

0.008

rs3793947

11

83,544,472

DLG2

G

A

0.570

0.073

0.011

3.72E-9

−0.010

0.016

0.525

rs4073221

3

18,277,488

SATB1

G

T

0.062

0.095

0.016

1.57E-8

0.007

0.023

0.754

rs4653767

1

226,916,078

ITPKB

T

C

0.726

0.083

0.011

1.63E-11

−0.005

0.017

0.756

rs4784227

16

52,599,188

TOX3

T

C

0.200

0.086

0.014

9.75E-11

−0.010

0.018

0.580

rs591323

8

16,697,091

MICU3

G

A

0.635

0.094

0.014

2.38E-11

−0.002

0.018

0.930

rs62120679

19

2,363,319

LSM7

T

C

0.426

0.077

0.014

6.64E-7

−0.004

0.022

0.843

rs6430538

2

135,539,967

TMEM163,CCNT2

C

T

0.189

0.117

0.011

8.24E-24

−0.047

0.017

0.006

rs6812193

4

77,198,986

FAM47E

C

T

0.687

0.083

0.011

1.43E-14

−0.017

0.016

0.310

rs76904798

12

40,614,434

LRRK2

T

C

0.132

0.140

0.015

1.21E-19

−0.016

0.022

0.483

rs78738012

4

114,360,372

ANK2, CAMK2D

C

T

0.039

0.122

0.018

4.78E-11

−0.012

0.029

0.680

rs8005172

14

88,472,612

GALC

T

C

0.434

0.077

0.012

8.77E-11

−0.021

0.016

0.171

rs8118008

20

3,168,166

DDRGK1

A

G

0.540

0.068

0.012

1.99E-6

0.014

0.018

0.432

rs823118

1

205,723,572

NUCKS1, SLC41A1

T

C

0.411

0.117

0.011

1.12E-23

−0.003

0.016

0.846

rs9468199

6

27,681,215

ZNF184

A

G

0.300

0.104

0.014

1.46E-12

0.044

0.022

0.046

  1. SNP single-nucleotide polymorphism, Chr Chromosome, Pos Position, EA Effect Allele, NEA Non-Effect Allele, EAF Effect Allele Frequency, PD Parkinson’s disease, AD Alzheimer’s disease, GWAS genome-wide association studies, SE standard error
  2. aFrequency of the effect allele in 1000 Genomes Project (CEU)
  3. bBeta is the regression coefficient based on the effect allele. Beta > 0 and Beta < 0 means that this effect allele regulates increased and reduced PD or AD risk, respectively
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BMC Medical Genetics

ISSN: 1471-2350

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