Table 3

Linear regression result for SNPs with CSF biomarkers in Normal, MCI and AD subjects (Top SNPs with p-value < 10-6)

Linear regression result without using covariates


Normal: Aβ1-42


Chromosome

SNP

Position

A1

TEST

BETA

STAT

P-value

Gene Symbol, Gene Name


15

rs2899472

49303347

A

GENO_2DF

NA

40.21

1.86E-09

CYP19A1, cytochrome p450, family 19, subfamily a, polypeptide 1

15

rs2899472

49303347

A

DOMDEV

0.1791

5.859

5.40E-08

CYP19A1, cytochrome p450, family 19, subfamily a, polypeptide 1

1

rs11206801

56623274

A

GENO_2DF

NA

33.14

6.37E-08

1

rs4431886

56624855

C

GENO_2DF

NA

33.14

6.37E-08

15

rs2899472

49303347

A

ADD

-0.1407

-5.699

1.11E-07

CYP19A1, cytochrome p450, family 19, subfamily a, polypeptide 1

19

rs2075650

50087459

G

GENO_2DF

NA

30.02

3.03E-07

TOMM40, translocase of outer mitochondrial membrane 40 homolog (yeast)

12

rs10784496

64447238

G

GENO_2DF

NA

29.98

3.09E-07

7

rs12534221

130938530

A

GENO_2DF

NA

27.83

9.04E-07

6

rs1727638

72196293

A

GENO_2DF

NA

27.69

9.71E-07


Normal: T-tau


Chromosome

SNP

Position

A1

TEST

BETA

STAT

P-value

Gene Symbol, Gene Name


12

rs1997111

117872301

T

GENO_2DF

NA

36.66

1.10E-08

12

rs11069178

117852210

C

GENO_2DF

NA

31.23

1.65E-07

2

rs17189298

119561787

A

GENO_2DF

NA

29.51

3.90E-07

8

rs2935776

109699079

C

GENO_2DF

NA

28.81

5.53E-07

8

rs2928826

109683270

T

GENO_2DF

NA

28.73

5.77E-07

2

rs895401

119584178

G

GENO_2DF

NA

27.86

8.90E-07

2

rs893769

119556554

C

ADD

-0.1024

-5.237

8.92E-07


Normal: P-tau181p


Chromosome

SNP

Position

A1

TEST

BETA

STAT

P-value

Gene Symbol, Gene Name


18

rs1943816

69209602

C

GENO_2DF

NA

32.09

1.08E-07

2

rs2074955

158686040

C

GENO_2DF

NA

32.06

1.09E-07

UPP2, uridine phosphorylase 2


MCI: T-tau


Chromosome

SNP

Position

A1

TEST

BETA

STAT

P-value

Gene Symbol, Gene Name


22

rs5998432

31075916

T

GENO_2DF

NA

27.91

8.696E-07


MCI: P-tau181p


Chromosome

SNP

Position

A1

TEST

BETA

STAT

P-value

Gene Symbol, Gene Name


2

rs7558386

227270383

G

GENO_2DF

NA

32.09

1.08E-07

2

rs7558386

227270383

G

DOMDEV

0.242

5.343

5.27E-07

3

rs7631605

37209593

T

GENO_2DF

NA

27.71

9.60E-07


AD: Aβ1-42


Chromosome

SNP

Position

A1

TEST

BETA

STAT

P-value

Gene Symbol, Gene Name


21

rs239713

27618347

T

GENO_2DF

NA

29.03

4.96E-07


AD: T-tau


Chromosome

SNP

Position

A1

TEST

BETA

STAT

P-value

Gene Symbol, Gene Name


20

rs4925189

59380439

G

DOMDEV

0.1969

5.178

6.35E-07

CDH4, cadherin 4, type 1, R-cadherin (retinal)


AD: P-tau181p


Chromosome

SNP

Position

A1

TEST

BETA

STAT

P-value

Gene Symbol, Gene Name


4

rs12643654

96378840

G

GENO_2DF

NA

29.04

4.95E-07

UNC5C, unc-5 homolog C (C. elegans)


Linear regression result using APOE genotype and age as covariates


Normal: Aβ1-42


Chromosome

SNP

Position

A1

TEST

BETA

STAT

P-value

Gene Symbol, Gene Name


15

rs2899472

49303347

A

GENO_2DF

NA

53.98

1.90E-12

CYP19A1, cytochrome p450, family 19, subfamily a, polypeptide 1

15

rs2899472

49303347

A

ADD

-0.1393

-6.925

3.85E- 0

CYP19A1, cytochrome p450, family 19, subfamily a, polypeptide 1

15

rs2899472

49303347

A

DOMDEV

0.1614

6.425

4.15E-09

CYP19A1, cytochrome p450, family 19, subfamily a, polypeptide 1

21

rs1022442

21277717

A

GENO_2DF

NA

30.21

2.75E-07

NCAM2, neural cell adhesion molecule 2

10

rs2493624

19102262

G

GENO_2DF

NA

28.61

6.14E-07

10

rs11015839

19042893

A

GENO_2DF

NA

28.51

6.45E-07

ARL5B, adp-ribosylation factor-like 5b

10

rs11015860

19045045

G

GENO_2DF

NA

28.51

6.45E-07

1

rs10911736

183689227

A

GENO_2DF

NA

28.16

7.69E-07

10

rs11015839

19042893

A

ADD

-0.1151

-5.257

7.87E-07

10

rs11015860

19045045

G

ADD

-0.1151

-5.257

7.87E-07

10

rs11015939

19057948

A

ADD

-0.1243

-5.219

9.25E-07

10

rs2495832

19114467

G

ADD

-0.1243

-5.219

9.25E-07

6

rs12203791

67778209

T

GENO_2DF

NA

27.68

9.76E-07

10

rs10763625

19074957

T

ADD

-0.124

-5.206

9.78E-07


Normal: T-tau


Chromosome

SNP

Position

A1

TEST

BETA

STAT

P-value

Gene Symbol, Gene Name


12

rs1997111

117872301

T

GENO_2DF

NA

30.74

2.11E-07

2

rs17189298

119561787

A

GENO_2DF

NA

27.92

8.66E-07

18

rs1021599

28469054

T

GENO_2DF

NA

27.88

8.81E-07


Normal: P-tau181p


Chromosome

SNP

Position

A1

TEST

BETA

STAT

P-value

Gene Symbol, Gene Name


18

rs1943816

69209602

C

GENO_2DF

NA

31.43

1.50E-07

2

rs2074955

158686040

C

GENO_2DF

NA

30.78

2.07E-07

UPP2, uridine phosphorylase 2


MCI: Aβ1-42


Chromosome

SNP

Position

A1

TEST

BETA

STAT

P-value

Gene Symbol, Gene Name


10

rs2986971

30136634

G

GENO_2DF

NA

31.88

1.20E-07

10

rs2986971

30136634

G

ADD

0.08328

5.228

8.88E-07


MCI: T-tau


Chromosome

SNP

Position

A1

TEST

BETA

STAT

P-value

Gene Symbol, Gene Name


4

rs2768975

48724658

G

GENO_2DF

NA

30.89

1.96E-07

FLJ21511, hypothetical protein flj21511

4

rs6850199

48695607

A

GENO_2DF

NA

29.93

3.18E-07

FLJ21511, hypothetical protein flj21511

18

rs1445093

48024821

C

GENO_2DF

NA

28.14

7.75E-07


MCI: P-tau181p


Chromosome

SNP

Position

A1

TEST

BETA

STAT

P-value

Gene Symbol, Gene Name


7

rs121724

29207970

G

GENO_2DF

NA

31.49

1.45E-07

CHN2, chimerin (chimaerin) 2

8

rs7842088

17629409

G

GENO_2DF

NA

30.73

2.12E-07

MTUS1, mitochondrial tumor suppressor 1


Abbreviations: SNP, single-nucleotide polymorphism; ADD, additive effects of allele dosage; DOMDEV, dominance deviation from additivity, rather specifying that a particular allele is dominant or recessive; GENO_2DF, a 2 df joint test of both additive and dominance; A1, tested allele (minor allele); BETA, regression coefficient; STAT, coefficient t-statistic

Han et al. BMC Neurology 2010 10:90   doi:10.1186/1471-2377-10-90

Open Data