Table 2 Most significant results for GFR (examination 7), UAE (examination 6), cysC (examination 7), and mean TSH (examinations 3 and 4) by GEE (2a), FBAT (2b) and linkage (2c) analyses

CysC

rs1158167

23,526,189

20

0.006

8.5*10^-09

CST9L|CST9|CST3

UAE

rs1712790

114,126,679

11

0.014

1.9*10^-06

FAM55B

TSH

rs6977660

19,578,720

7

0.010

3.7*10^-06

TSH

rs9322817

105,338,926

6

0.502

6.5*10^-06

HACE1

TSH

rs10499559

21,882,699

7

0.068

8.3*10^-06

RAPGEF5

UAE

rs9305354

28,397,067

21

0.013

8.4*10^-06

CysC

rs2145231

23,573,547

20

0.011

1.1*10^-05

CST9|CST3|CST4

UAE

rs723464

133,940,196

4

0.000

1.1*10^-05

UAE

rs2113379

207,177,180

2

0.003

1.4*10^-05

ADAM23

GFR

rs2839235

46,625,020

21

0.055

1.6*10^-05

PCNT2

TSH

rs10493147

129,095,104

4

0.040

2.1*10^-05

HSPA4L

TSH

rs784490

39,148,534

3

0.005

2.8*10^-05

TTC21A

UAE

rs278021

6,698,929

1

0.958

2.9*10^-05

DNAJC11

UAE

rs1856190

33,598,615

9

0.127

3.0*10^-05

UAE

rs10485409

91,562,132

6

0.147

3.1*10^-05

UAE

rs2785980

216,088,914

1

4.8*10^-04

3.7*10^-05

UAE

rs837678

191,168,583

3

0.012

3.8*10^-05

LEPREL1

GFR

rs3095160

49,844,269

13

0.002

3.8*10^-05

UAE

rs2761171

99,278,898

13

0.078

4.1*10^-05

CLYBL

GFR

rs10507344

24,623,069

13

0.017

4.1*10^-05

PABPC3

GFR

rs890945

157,924,801

5

0.036

4.7*10^-05

UAE

rs10502192

114,127,562

11

0.051

4.9*10^-05

FAM55B

GFR

rs10489639

157,492,600

1

0.194

4.9*10^-05

CD48

TSH

rs9308765

118,759,439

2

0.353

5.1*10^-05

TSH

rs3908399

12,849,275

20

8.0*10^-04

5.2*10^-05

2b. Top 25 SNPs for association with GFR (examination 7), UAE (examination 6), cysC (examination 7), and mean TSH (examinations 3 and 4) based on the lowest p-value of the FBAT test. Corresponding phenotype names on the web are GFRMV7 (GFR), UAELNMV6 (UAE), CYSCMV7 (CysC), and TSHMEAN34MV (TSH)

TRAIT

SNP

Physical Location (Mb)

Chromosome

P value - FBAT

P value - GEE

GENE

GEE

GENE

UAE

rs1243400

9,016,664

10

4.8*10^-06

0.036

UAE

rs827640

9,028,017

10

1.5*10^-05

0.047

UAE

rs7315682

32,577,224

12

2.1*10^-05

0.28

FGD4

GFR

rs6434804

196,589,899

2

2.4*10^-05

0.003

DNAH7

UAE

rs1543468

230,655,160

1

2.5*10^-05

0.253

SLC35F3

UAE

rs723464

133,940,196

4

2.7*10^-05

1.0*10^-05

TSH

rs4128956

131,848,063

9

3.6*10^-05

0.355

TSH

rs7865184

14,677,867

9

3.9*10^-05

0.082

ZDHHC21

CysC

rs563754

61,068,849

18

4.7*10^-05

0.002

GFR

rs2885618

41,244,839

18

4.8*10^-05

1.0*10^-04

TSH

rs701801

100,166,859

10

5.8*10^-05

0.090

HPS1

UAE

rs33855

171,124,642

5

6.2*10^-05

0.192

GFR

rs10483741

61,059,454

14

6.3*10^-05

0.298

PRKCH

CysC

rs2121267

46,461,040

2

6.6*10^-05

0.002

EPAS1

CysC

rs1400306

83,256,163

11

7.2*10^-05

0.061

TSH

rs1223531

13,255,521

6

8.0*10^-05

0.123

PHACTR1

CysC

rs10504244

59,147,328

8

8.3*10^-05

0.005

UAE

rs2374688

106,175,669

12

9.1*10^-05

0.087

BTBD11

UAE

rs10519012

58,333,458

15

1.0*10^-04

0.088

CysC

rs1931619

82,682,388

6

1.0*10^-04

0.05

UAE

rs10501264

41,387,406

11

1.1*10^-04

7.2*10^-04

UAE

rs10492025

111,735,770

12

1.1*10^-04

0.41

RPH3A

UAE

rs2056694

128,517,768

7

1.1*10^-04

0.1

UAE

rs8113386

16,332,871

19

1.1*10^-04

0.053

KLF2

TSH

rs295136

200,966,508

2

1.3 *10^-04

0.64

2c. Magnitude and Location of Peak LOD scores for regions in which LOD exceeds 2.5.* Corresponding phenotype names on the web are PHOSPHORUSMV2 (serum phosphorous), URICACIDMV2 (uric acid), SCRLNMVNL6 (serum creatinine exam 6), LHMV3 (luteinizing hormone), GFRMVNL6 (GFR exam 6), CALCIUMMV2 (serum calcium), GFRMV7 (GFR exam 7), and SCRLNMVNL5 (serum creatinine exam 5)

Trait

Serum Phosphorous

Uric acid

Serum creatinine (exam 6)

Luteinizing Hormone

GFR (exam 6)

Serum Calcium

GFR (exam 7)

Serum creatinine (exam 5)