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Table 3 Combination of FBAT and GEE, for grouped BMD phenotypes*

From: Genome-wide association with bone mass and geometry in the Framingham Heart Study

3a: Combination of FBAT and GEE, for grouped BMD phenotypes in men and women combined

Chrom

Physical Position

SNP

Min p-value by GEE

Min p-value by FBAT

% Significant P-values by GEE & FBAT**

Function

Gene symbol

1

177,489,285

rs7544774

3.34 × 10-4

7.55 × 10-3

67

intron

XPR1

1

231,181,475

rs7554650

1.67 × 10-4

5.93 × 10-3

67

unknown

 

2

6,719,916

rs7584788

7.55 × 10-3

5.19 × 10-4

67

unknown

 

2

15,963,228

rs2380707

1.14 × 10-3

5.22 × 10-4

67

unknown

 

2

79,078,098

rs1261226

1.19 × 10-5

4.47 × 10-3

67

unknown

 

4

177,742,191

rs9312601

2.22 × 10-3

7.03 × 10-4

67

unknown

 

4

181,139,118

rs10520437

5.23 × 10-4

7.72 × 10-5

100

unknown

 

4

181,162,903

rs922028

8.45 × 10-4

1.53 × 10-5

100

unknown

 

5

26,917,842

rs1479679

1.13 × 10-4

2.38 × 10-4

67

intron

CDH9

5

53,527,854

rs16882423

1.65 × 10-3

2.38 × 10-3

67

intron

ARL15

7

9,739,152

rs1557978

1.73 × 10-4

3.97 × 10-4

33

intron

 

7

11,301,740

rs10486135

1.67 × 10-4

5.95 × 10-4

67

intron

 

7

18,183,021

rs10486301

1.94 × 10-4

9.43 × 10-4

67

unknown

 

8

114,092,330

rs1156075

5.55 × 10-3

8.51 × 10-3

67

intron

CSMD3

11

95,219,586

rs546809

1.41 × 10-3

7.10 × 10-5

67

intron

MTMR2

12

103,526,872

rs10507180

7.18 × 10-4

4.16 × 10-3

100

intron

CHST11

16

76,268,225

rs8051539

2.08 × 10-3

5.80 × 10-3

67

unknown

 

18

48,132,968

rs768207

1.94 × 10-3

2.99 × 10-3

67

intron

DCC

19

42,607,072

rs1465434

1.51 × 10-3

7.17 × 10-4

67

intron

ZNF569

21

39,078,994

rs1209926

2.51 × 10-4

3.21 × 10-5

33

unknown

C21orf24/ETS2

3b: Sex-specific results for grouped BMD phenotypes

Chrom

Physical Position

SNP

Sex

Min p-value by GEE

Min p-value by FBAT

Function

Gene symbol

1

48,261,693

rs560004

Males

8.91 × 10-4

3.48 × 10-3

unknown

 

1

200,641,877

rs1935588

Females

6.14 × 10-4

7.62 × 10-4

unknown

 

2

125,809,045

rs1215318

Males

1.23 × 10-4

2.96 × 10-4

unknown

 

4

181,162,903

rs922028

Females

1.61 × 10-4

6.16 × 10-3

unknown

 

5

26,917,842

rs1479679

Females

4.36 × 10-5

6.96 × 10-3

intron

CDH9

6

47,657,085

rs9296566

Females

2.27 × 10-4

5.08 × 10-4

intron

CD2AP

6

83,666,784

rs9294266

Males

5.32 × 10-4

2.01 × 10-3

intron

C6orf157

7

33,440,554

rs10486541

Males

1.54 × 10-5

1.95 × 10-3

unknown

 

7

35,084,096

rs10486661

Females

9.34 × 10-6

9.98 × 10-5

unknown

TBX20

9

20,592,188

rs7867710

Females

6.96 × 10-4

2.97 × 10-3

intron

MLLT3

9

88,679,511

rs1779308

Males

3.09 × 10-3

4.94 × 10-3

unknown

 

11

96,720,041

rs10501872

Females

4.03 × 10-4

1.02 × 10-3

unknown

 

12

20,059,354

rs10505843

Females

2.02 × 10-4

7.38 × 10-3

unknown

 

13

52,997,850

rs9316628

Females

2.51 × 10-3

5.22 × 10-4

unknown

 

13

107,573,163

rs1223978

Males

3.42 × 10-4

5.07 × 10-4

unknown

 

15

55,974,260

rs10518945

Females

6.19 × 10-5

6.15 × 10-4

unknown

ALDH1A2

17

11,054,857

rs2024134

Males

4.75 × 10-3

6.31 × 10-5

unknown

 

17

53,546,007

rs181224

Males

2.15 × 10-5

2.90 × 10-3

unknown

Dlc2/OR4D1/OR4D2

18

48,132,968

rs768207

Females

1.35 × 10-4

2.57 × 10-4

intron

DCC

20

18,310,297

rs2328293

Females

7.74 × 10-4

4.35 × 10-3

locus

C20orf12

  1. * Femoral neck, Trochanter, Lumbar spine BMD
  2. ** Percentage of traits nominally significantly associated with the SNP at p < 0.01 in both GEE and FBAT
  3. Subsamples with N < 400 excluded.
  4. Percentage of traits nominally significantly associated at p < 0.01 in both GEE and FBAT was 67% for all SNPs.