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Table 2 Structural and Functional Brain Aging (MRI and Cognitive Testing) Phenotypes† for FHS 100K Project: Results of Association and Linkage Analyses

From: Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham study

2, section a: GEE, Top 25 p-values

Phenotype

SNP

Chromosome

Physical location

GEE p-value

FBAT p-value

Gene Region (within 60 kb)

ATCBV

rs1970546

20

59287333

4.0 × 10-8

0.005

CDH4

F3

rs2179965*

1

88514033

1.1 × 10-6

0.013

 

Nam

rs1155865

4

67562623

1.6 × 10-6

0.554

 

F3

rs2832077

21

29062892

1.8 × 10-6

0.007

 

F2

rs2352904

14

48442551

2.1 × 10-6

0.012

 

F2

rs6914079*

6

14704344

2.2 × 10-6

0.018

 

F2

rs9325032

5

146395409

2.8 × 10-6

0.008

 

ALLV

rs2847476

11

113696226

3.0 × 10-6

0.001

NNMT

Sim

rs3891355

12

105453162

3.2 × 10-6

0.089

POLR3B, RFX4

ATBV

rs5028798

11

34562011

3.3 × 10-6

0.394

EHF

Nam

rs530965

11

78742749

3.5 × 10-6

0.119

 

Nam

rs9303401

17

54202944

4.9 × 10-6

0.099

PPM1E

AFBV

rs952700

11

99090946

5.7 × 10-6

0.003

CNTN5

F3

rs1031381

11

133593892

6.0 × 10-6

0.075

NCAPD3

F2

rs10489896*

1

230890353

6.2 × 10-6

0.109

TARBP1

WRAT

rs9300212

12

33592433

8.2 × 10-6

0.002

 

Nam

rs1831521

9

90488911

8.4 × 10-6

0.002

DIRAS2

F3

rs934299

2

137172672

9.0 × 10-6

0.318

 

ALTHBV

rs360929

4

153265305

9.1 × 10-6

0.055

 

F2

rs2893363

7

29952294

9.6 × 10-6

0.812

C7orf41

WRAT

rs10502991

18

50243287

1.0 × 10-5

0.001

 

APBV

rs2769965

9

79048598

1.1 × 10-5

0.012

 

APBV

rs719435

7

31324796

1.1 × 10-5

0.188

CCDC129

F1

rs9292769

5

40433668

1.1 × 10-5

0.163

 

Nam

rs10506718

12

75377929

1.1 × 10-5

0.402

 

2, section b: FBAT, Top 25 p-values

Trait

SNP

Chromosome

Physical location

GEE p-value

FBAT p-value

Gene Region(s) (within 60 kb)

ALLV

rs7124781

11

42513374

0.008

2.0 × 10-7

 

Sim

rs1131497

11

121007955

0.008

3.2 × 10-6

SORL1

WRAT

rs10506065

12

30342307

0.050

5.0 × 10-6

 

AFBV

rs3852286

7

140126618

0.145

6.5 × 10-6

BRAF and MRPS33

WRAT

rs4529807

10

22358107

0.013

1.1 × 10-5

DNAJC1

F3

rs847342

14

71805791

0.441

1.3 × 10-5

RGS6

AFBV

rs719775

3

64366493

0.001

1.8 × 10-5

 

Sim

rs936111

15

99376659

0.014

2.1 × 10-5

LRRK1

ATBV

rs2143881

6

50960846

0.077

2.1 × 10-5

TFAP2B

AHPV

rs9293140

5

24643203

0.092

2.1 × 10-5

CDH10

AFBV

rs9288446*

2

212907533

0.001

2.3 × 10-5

ERBB4

APBV

rs1472962

4

95949555

0.004

3.1 × 10-5

PDLIM5

ATBV

rs2793772

13

99029574

0.047

3.3 × 10-5

CLYBL

F2

rs1333583

13

82037151

0.031

3.4 × 10-5

 

ATBV

rs10497352

2

170781278

0.005

3.6 × 10-5

ZNF650

F1

rs497836

13

93605509

0.020

3.8 × 10-5

GPC6

APBV

rs6459928

7

158428045

0.271

4.0 × 10-5

VIPR2

AHPV

rs1963442

3

75872661

0.046

4.3 × 10-5

ZNF717

APBV

rs10503238

8

4027465

0.002

4.4 × 10-5

 

F2

rs2861215

2

77958447

0.006

4.7 × 10-5

 

Nam

rs9311168

3

37952421

0.067

4.9 × 10-5

CTDSPL

F2

rs2029395

2

1.8 × 10-8

0.027

4.9 × 10-5

TTN, FLJ39502

ATCBV

rs10510717

3

41307494

0.005

5.0 × 10-5

CTNNB1

ATBV

rs1433527

2

1.8 × 10-8

0.028

5.1 × 10-5

DDX18

2, section c: Linkage Peaks with LOD scores ≥ 2.0.

Trait

SNP closest to linkage peak

Chromosome

Physical location

1.5 – LOD support interval start

1.5 – LOD support interval end

LOD score

WATBV†

rs1547275

9

79548023

76128637

86702472

2.81

WF3†

rs2975420

8

19534278

12651557

22836499

2.20

WNam†

rs2765241

1

62439617

59085658

67006164

2.95

WNam†

rs293966

11

26536069

21237681

33363547

2.14

WWRAT†

rs10512187

9

87400439

84893406

110115339

2.04

WWRAT†

rs1328822

13

93605666

87815515

97536766

2.50

WWRAT†

rs1846090

18

14573728

13423610

19583575

5.10

WWRAT†

rs10518241

19

3540074

1888178

6189414

2.33

BMRIZLWMHVMV

rs4426714

4

5052671

105905

9505355

2.20

BMRIZLWMHVMV

rs236535

17

65788911

59677087

68475624

2.09

  1. Autosomal SNPs with genotypic call rate ≥ 80%, minor allele frequency ≥ 10%, Hardy-Weinberg test p ≥ 0.001, and ≥10 informative families for FBAT. Genes in bold are highlighted in discussion
  2. *Indicates a similar result for this trait was observed (but not shown) for a SNP with r2 = 1 to the reported SNP
  3. †Winsorized residuals were analyzed, hence trait names are prefixed with a 'W'; linkage results in bold are highlighted in the discussion
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BMC Medical Genetics

ISSN: 1471-2350

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