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Table 2 Summary of PSP GWAS and PSP meta-analysis

From: Replication of progressive supranuclear palsy genome-wide association study identifies SLCO1A2 and DUSP10 as new susceptibility loci

      

GWAS Hoglinger et al. (EUR only)

New Mayo case-control population

Meta-analysis

      

GWAS Stage 1

GWAS Stage 2

Joint Analysis

SNP ID

chr

GRCh38 location

Gene or nearby gene

Major allele

Minor allele

MAF cases

MAF control

MAF cases

MAF control

OR

PJ

MAF cases

MAF control

OR (95% CI)

P

OR (95% CI)

P

OR Direction

rs8070723

17

46,003,698

MAPT

A

G

0.051

0.235

0.060

0.232

5.46

1.5E-116

0.049

0.233

5.74 (4.24–7.78)

1.9E-29

5.51 (4.83–6.28)

5.57E-144

++

rs242557

17

45,942,346

MAPT

G

A

0.530

0.348

0.495

0.355

0.51

4.2E-70

0.585

0.403

0.52 (0.45–0.61)

1.2E-18

0.51 (0.48–0.55)

3.78E-85

–

rs1768208

3

39,481,512

MOBP

G

A

0.357

0.286

0.353

0.287

0.72

1.0E-16

0.389

0.264

0.56 (0.48–0.66)

6.6E-13

0.69 (0.64–0.74)

3.48E-26

–

rs12203592

6

396,321

IRF4

C

T

0.164

0.200

0.131

0.198

1.49

6.2E-15

0.159

0.173

1.09 (0.89–1.33)

3.9E-01

1.40 (1.28–1.53)

2.31E-13

++

rs7571971

2

88,595,833

EIF2AK3

C

T

0.314

0.257

0.307

0.248

0.75

3.2E-13

0.320

0.291

0.88 (0.75–1.03)

1.0E-01

0.77 (0.72–0.83)

2.76E-13

–

rs1411478

1

180,993,146

STX6

G

A

0.496

0.418

0.464

0.426

0.79

2.3E-10

0.473

0.410

0.77 (0.66–0.89)

4.4E-04

0.79 (0.74–0.84)

7.17E-13

–

rs11568563

12

21,304,500

SLCO1A2

A

C

0.078

0.053

0.077

0.055

0.69

2.0E-07

0.089

0.053

0.60 (0.45–0.80)

4.2E-04

0.67 (0.59–0.76)

5.26E-10

–

rs6687758

1

221,991,606

DUSP10

A

G

0.229

0.189

0.227

0.191

0.8

2.8E-07

0.230

0.192

0.80 (0.67–0.96)

1.7E-02

0.80 (0.74–0.86)

1.14E-08

–

rs197971

6

23,586,904

LOC105374976

G

A

0.403

0.453

0.410

0.448

1.18

6.7E-06

0.395

0.422

1.13 (0.97–1.32)

1.1E-01

1.17 (1.10–1.25)

2.69E-06

++

rs2107272

7

43,156,788

HECW1

C

T

0.342

0.296

0.325

0.301

0.85

3.6E-05

0.332

0.295

0.83 (0.71–0.98)

2.5E-02

0.85 (0.79–0.91)

3.04E-06

–

rs6846520

4

83,097,119

PLAC8

G

A

0.071

0.109

0.089

0.108

1.35

3.9E-06

0.085

0.094

1.14 (0.88–1.47)

3.3E-01

1.30 (1.16–1.46)

4.87E-06

++

rs12744678

1

204,967,707

NFASC

C

T

0.331

0.280

0.302

0.287

0.86

2.1E-04

0.319

0.273

0.80 (0.68–0.94)

5.6E-03

0.85 (0.79–0.91)

6.22E-06

–

rs4733780

8

130,284,009

ASAP1

T

C

0.454

0.423

0.446

0.414

0.86

3.2E-05

0.457

0.429

0.89 (0.77–1.03)

1.1E-01

0.86 (0.81–0.92)

9.94E-06

–

rs6852535

4

122,557,561

IL2/IL21

G

A

0.289

0.338

0.277

0.322

1.24

9.2E-08

0.296

0.283

0.93 (0.79–1.09)

3.8E-01

1.17 (1.09–1.26)

1.11E-05

+−

rs10509119

10

60,052,882

ANK3

T

C

0.131

0.110

0.133

0.112

0.80

4.1E-05

0.130

0.113

0.83 (0.67–1.04)

1.1E-01

0.81 (0.73–0.89)

1.29E-05

–

rs11902595

2

48,456,607

PPP1R21

T

G

0.146

0.180

0.159

0.180

1.22

8.3E-05

0.161

0.184

1.21 (0.99–1.47)

6.1E-02

1.21 (1.11–1.33)

1.41E-05

++

rs2142991

10

42,845,657

BMS1/

LOC101929445

T

C

0.139

0.173

0.139

0.169

1.30

4.9E-07

0.156

0.150

0.95 (0.77–1.16)

6.0E-01

1.22 (1.11–1.34)

2.13E-05

+−

rs406113

6

28,515,705

GPX6

T

G

0.340

0.297

0.343

0.311

0.86

6.9E-05

0.339

0.314

0.90 (0.78–1.06)

2.0E-01

0.87 (0.81–0.93)

3.31E-05

–

rs4814911

20

19,863,250

RIN2

G

A

0.225

0.190

0.212

0.193

0.84

7.7E-05

0.214

0.195

0.89 (0.75–1.07)

2.3E-01

0.85 (0.78–0.92)

4.40E-05

–

rs17199690

16

25,420,834

LOC105371146

G

A

0.172

0.137

0.160

0.136

0.80

1.3E-05

0.144

0.139

0.97 (0.79–1.21)

8.2E-01

0.83 (0.76–0.91)

4.41E-05

–

rs895606

9

85,388,753

NTRK2/

AGTPBP1

C

T

0.496

0.444

0.472

0.449

0.86

3.1E-05

0.475

0.465

0.96 (0.83–1.12)

6.2E-01

0.88 (0.82–0.94)

5.74E-05

–

rs11532787

7

119,661,732

ANKRD7/KCND2

G

A

0.138

0.112

0.121

0.109

0.81

1.9E-04

0.116

0.102

0.86 (0.68–1.08)

1.9E-01

0.82 (0.74–0.91)

9.73E-05

–

rs3017756

11

95,804,194

CEP57

C

T

0.482

0.426

0.438

0.429

0.86

6.6E-05

0.428

0.418

0.95 (0.82–1.10)

5.0E-01

0.88 (0.82–0.94)

9.96E-05

–

rs11028138

11

24,751,636

LUZP2

T

C

0.102

0.081

0.085

0.068

0.75

6.8E-06

0.085

0.089

1.08 (0.83–1.41)

5.7E-01

0.80 (0.71–0.90)

1.42E-04

−+

rs13025979

2

186,000,879

LOC107985783

C

T

0.099

0.074

0.098

0.077

0.75

3.9E-06

0.080

0.088

1.15 (0.87–1.51)

3.3E-01

0.80 (0.72–0.90)

1.60E-04

−+

rs10083119

12

125,824,612

TMEM132B/

LOC101927464

G

A

0.126

0.096

0.119

0.103

0.80

8.0E-05

0.112

0.106

0.95 (0.75–1.20)

6.6E-01

0.83 (0.75–0.91)

2.07E-04

–

rs4890490

18

44,857,303

SETBP1

C

T

0.436

0.385

0.413

0.402

0.88

9.0E-04

0.434

0.410

0.89 (0.77–1.03)

1.2E-01

0.89 (0.83–0.95)

2.76E-04

–

rs1433277

10

125,584,032

TEX36

G

T

0.431

0.472

0.433

0.466

1.17

2.1E-05

0.460

0.450

0.96 (0.83–1.12)

6.1E-01

1.13 (1.06–1.20)

3.24E-04

+−

rs4256646

9

73,182,919

ANXA1/

LOC101927281

T

C

0.458

0.509

0.466

0.490

1.16

9.6E-05

0.484

0.491

1.02 (0.88–1.18)

8.1E-01

1.13 (1.06–1.20)

3.33E-04

++

rs2075650

19

44,892,362

TOMM40

T

C

0.112

0.141

0.117

0.140

1.26

2.8E-05

0.144

0.138

0.96 (0.77–1.19)

6.9E-01

1.19 (1.08–1.32)

3.99E-04

+−

rs9783599

14

77,970,692

ADCK1

NRXN3

C

A

0.494

0.443

0.471

0.446

0.87

9.6E-05

0.469

0.475

1.05 (0.90–1.21)

5.4E-01

0.90 (0.84–0.96)

9.93E-04

−+

rs4742987

9

106,119,937

TMEM38B/

LOC100996590

T

C

0.393

0.359

0.389

0.364

0.86

6.8E-05

0.368

0.380

1.05 (0.90–1.22)

5.1E-01

0.89 (0.84–0.96)

1.08E-03

−+

rs1001408

12

66,898,508

GRIP1

A

G

0.119

0.086

0.103

0.095

0.81

5.1E-04

0.101

0.097

0.96 (0.76–1.23)

7.7E-01

0.84 (0.75–0.93)

1.15E-03

–

rs10197080

2

223,231,568

KCNE4/RN7SL807P

G

T

0.113

0.082

0.095

0.087

0.79

1.3E-04

0.100

0.104

1.08 (0.85–1.38)

5.2E-01

0.84 (0.75–0.94)

1.71E-03

−+

rs4768559

12

44,576,131

NELL2

T

G

0.262

0.209

0.224

0.214

0.85

2.1E-04

0.199

0.209

1.06 (0.89–1.28)

5.1E-01

0.89 (0.82–0.96)

1.77E-03

−+

rs217727

11

1,995,678

MRPL23/IGF2

G

A

0.218

0.178

0.189

0.177

0.85

3.5E-04

0.179

0.184

1.03 (0.85–1.24)

7.9E-01

0.88 (0.81–0.95)

2.02E-03

−+

rs7104402

11

43,019,438

LOC100507205/HNRNPKP3

C

T

0.323

0.281

0.302

0.290

0.87

6.2E-04

0.301

0.319

1.08 (0.92–1.27)

3.4E-01

0.91 (0.85–0.98)

8.58E-03

−+

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Molecular Neurodegeneration

ISSN: 1750-1326