Table 3 Results of gene-based GWAS analysis.

From: Systematic Analysis and Biomarker Study for Alzheimer’s Disease

Entrez Gene

Name

CHR

#SNPS

BF.pval

Blood AD FC

Blood AD BH.pval

Blood MCI FC

Blood MCI BH.pval

Brain AD FC

Brain AD BF.pval

10452

TOMM40*

19

139

2.72E-150

1.03

0.14

1.06

6.87E-04

0.92

1.00

341

APOC1

19

82

2.70E-135

1.00

0.67

1.01

0.25

1.27

0.85

348

APOE*

19

97

1.52E-131

    

1.12

1.00

5819

PVRL2

19

268

3.34E-125

0.99

0.52

1.03

0.43

1.05

1.00

4059

BCAM

19

129

1.60E-38

1.00

0.69

1.00

0.73

1.04

1.00

5971

RELB

19

115

1.32E-14

1.08

6.64E-07

1.08

1.79E-05

1.00

1.00

602

BCL3

19

141

4.10E-13

1.07

1.41E-02

1.07

2.25E-02

1.27

6.18E-05

388551

CEACAM16

19

171

1.16E-11

    

1.02

1.00

346

APOC4

19

102

4.23E-10

    

1.04

1.00

1209

CLPTM1

19

198

1.39E-09

1.08

8.21E-05

1.15

1.25E-10

0.96

1.00

90332

EXOC3L2

19

148

3.12E-09

1.00

0.80

1.00

0.76

1.00

1.00

344

APOC2

19

105

1.06E-08

    

1.02

1.00

1191

CLU*

8

148

2.15E-08

1.00

0.96

1.00

0.83

1.31

1.12E-05

79090

TRAPPC6A

19

94

4.14E-08

0.99

0.62

1.01

0.46

0.93

0.02

2041

EPHA1*

7

125

6.05E-08

1.01

0.57

1.03

0.092

1.01

1.00

284353

NKPD1

19

73

9.90E-08

    

0.97

1.00

643680

MS4A4E

11

206

9.86E-07

      

8301

PICALM*

11

396

1.06E-06

1.01

0.55

0.93

1.90E-02

0.95

1.00

11129

CLASRP

19

111

1.27E-06

1.01

0.32

1.00

0.79

1.18

1.00

388552

BLOC1S3

19

70

1.49E-06

    

0.98

1.00

284352

PPP1R37

19

216

1.95E-06

    

0.97

1.00

64231

MS4A6A*

11

102

2.15E-06

0.89

4.16E-04

0.83

5.25E-07

1.43

0.00

5817

PVR

19

125

3.92E-06

1.00

0.78

1.01

0.20

0.96

1.00

2206

MS4A2

11

131

5.56E-06

0.99

0.48

0.98

0.22

0.98

1.00

51338

MS4A4A*

11

201

6.82E-06

0.98

1.08E-02

0.97

1.14E-05

1.44

3.38E-07

10347

ABCA7*

19

234

8.97E-06

1.17

7.97E-10

1.19

2.68E-09

1.13

2.47E-03

1378

CR1*

1

373

2.01E-05

1.08

9.70E-05

1.05

1.39E-02

1.03

1.00

23624

CBLC

19

118

2.83E-05

    

1.00

1.00

274

BIN1*

2

348

2.95E-05

1.04

0.11

1.11

1.81E-04

0.96

1.00

147710

IGSF23

19

155

3.08E-05

    

0.99

1.00

338398

TAS2R60

7

76

6.74E-05

    

1.00

1.00

79760

GEMIN7

19

138

7.40E-05

0.99

0.21

1.00

0.53

0.87

1.00

1839

HBEGF

5

77

9.99E-05

1.00

0.99

1.00

0.66

1.07

1.00

7791

ZYX

7

100

2.52E-04

1.13

1.51E-05

1.18

2.42E-07

1.03

1.00

23526

HMHA1

19

221

2.92E-04

1.09

3.77E-06

1.14

7.87E-10

1.20

4.05E-07

56971

CEACAM19

19

117

3.03E-04

1.01

0.14

1.00

0.56

1.07

1.00

1379

CR1L

1

420

4.27E-04

    

1.04

1.00

162979

ZNF296

19

98

4.85E-04

1.04

4.03E-02

1.10

2.34E-07

1.00

1.00

23403

FBXO46

19

82

9.57E-04

1.05

5.69E-06

1.08

5.47E-07

1.05

1.00

6653

SORL1*

11

354

1.25E-03

1.21

2.80E-08

1.31

1.02E-12

0.89

1.00

6688

SPI1

11

127

2.33E-03

1.13

3.72E-05

1.13

5.42E-04

1.09

1.00

3122

HLA-DRA

6

722

2.46E-03

0.95

0.076

0.90

1.43E-03

1.40

9.51E-08

3123

HLA-DRB1*

6

1550

2.83E-03

0.93

0.68

1.08

0.65

1.41

2.25E-03

1265

CNN2

19

203

2.88E-03

1.03

0.50

1.06

0.08

1.23

2.69E-03

245802

MS4A6E

11

200

3.10E-03

    

1.05

1.00

1135

CHRNA2

8

191

3.61E-03

1.03

0.21

1.06

3.74E-03

1.00

1.00

92154

MTSS1L

16

172

3.74E-03

    

1.24

1.16E-02

399888

FAM180B

11

35

5.27E-03

1.00

0.52

1.00

0.73

1.03

1.00

114971

PTPMT1

11

43

5.58E-03

    

0.92

1.00

4722

NDUFS3*

11

41

7.22E-03

0.90

7.38E-10

0.90

1.78E-08

0.86

1.32E-02

388553

BHMG1

19

76

7.26E-03

    

1.03

1.00

55709

KBTBD4

11

37

7.75E-03

1.02

0.087

1.02

3.74E-02

0.88

3.63E-02

945

CD33*

19

119

7.75E-03

1.04

0.058

1.03

0.17

1.22

9.72E-07

1762

DMWD

19

89

9.46E-03

1.05

1.56E-04

1.06

1.40E-06

0.96

1.00

2185

PTK2B*

8

486

1.00E-02

1.06

2.19E-03

1.03

0.15

0.99

1.00

23788

MTCH2*

11

71

1.02E-02

1.00

0.66

1.00

0.71

0.86

1.00

55697

VAC14

16

274

1.57E-02

1.04

8.06E-05

1.06

1.76E-08

0.99

1.00

1760

DMPK

19

73

2.21E-02

1.00

0.72

1.01

2.60E-02

1.09

1.00

23607

CD2AP*

6

451

2.37E-02

0.99

0.12

0.97

1.53E-03

1.15

4.08E-07

3117

HLA-DQA1

6

2022

2.42E-02

0.92

0.14

0.98

0.74

1.20

1.00

932

MS4A3

11

142

2.46E-02

0.91

1.42E-03

0.88

1.58E-04

0.96

1.00

147912

SIX5

19

60

2.48E-02

1.00

0.84

1.01

0.19

1.27

1.92E-04

114900

C1QTNF4

11

38

2.83E-02

    

0.82

1.89E-03

23360

FNBP4

11

140

3.08E-02

0.98

0.58

0.96

0.19

1.00

1.00

56244

BTNL2

6

613

3.48E-02

    

1.01

1.00

28955

DEXI

16

138

4.19E-02

1.00

0.88

1.02

0.18

1.03

1.00

79841

AGBL2

11

128

4.83E-02

    

1.00

1.00

  1. This table lists 67 genes identified by MAGMA (BF.pval < 0.05) from the IGAP stage 1 GWAS dataset, and compares their expression (fold-change and p-value) in AD and MCI blood datasets, and in the brain dataset from our previous study7. AD GWAS risk genes are marked with an asterisk, “*”. The chromosome and the number of SNPs for each of these genes within 20 kbp up- and downstream regions are shown in the third and fourth columns. BF.pval indicates Bonferroni corrected p-value, while BH.pval indicates Benjamini & Hochberg corrected p-value.
Back to article page