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Table 3 Comparison of SNP allele frequencies of the studied Caucasian sample with the data on Caucasians from databases and literature

From: Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and osteoporosis

Gene

SNP

Reference population

Database or reference

Data from a database or reference

Caucasiansa

 
    

Frequencyb

n

Frequency

n

 

APOE

1

American Caucasians

[53]

0.33

220

0.357

1,862

0.48

 

2

American Caucasians

dbSNP

0.33

24

0.399

1,839

0.64

  

Europeans from North Karelia, Finland

dbSNP

0.4

24

0.399

1,839

0.84

 

3

European-Americans

dbSNP

0.12

24

0.149

1,858

0.91

  

Caucasiansc

HGVbase

0.16

152

0.149

1,858

0.81

  

Europeans from North Karelia, Finland

dbSNP

0.23

24

0.149

1,858

0.37

 

4

European-Americans

dbSNP

0.19

24

0.087

1,783

0.16

  

Caucasiansc

HGVbase

0.08

152

0.087

1,783

0.87

  

Europeans from North Karelia, Finland

dbSNP

0.04

24

0.087

1,783

0.25

COL1 α1

5

White women with Spanish ancestors

[54]

0.13

256

0.154

1,856

0.36

 

6

American Caucasians

[31]

0.187

637

0.188

1,855

0.98

ER-α

9

Australian females

[55]

0.44

125

0.484

1,861

0.39

  

Greek males

[56]

0.49

50

0.484

1,861

0.95

 

10

American females

[57]

0.45

253

0.449

1,861

0.96

  

Finnish females

[58]

0.42

322

0.449

1,861

0.38

 

11

SANGER 12 DNAs of Caucasian origin

dbSNP

0.08

12

0.257

1,857

0.32

 

12

Australian females

[55]

0.23

120

0.218

1,859

0.84

  

Slovenian females

[59]

0.3

85

0.218

1,859

0.10

  

Caucasiansc

dbSNP

0.27

31

0.218

1,859

0.59

 

13

Caucasiansc

HGVbase

0.08

42

0.098

1,863

1.00

 

15

Caucasiansc

dbSNP

0.18

31

0.203

1,863

0.90

IL-6

16

Caucasians

dbSNP

0.5

31

0.434

1,860

0.58

  

English

[60]

0.57

2,560

0.434

1,860

<0.01

  

Italians

[61]

0.45

183

0.434

1,860

0.74

  

Spaniards

[62]

0.56

118

0.434

1,860

0.01

  

Finns

HGVbase

0.46

400

0.434

1,860

0.37

  

Finns

HGVbase

0.48

50

0.434

1,860

0.62

  

Finns

HGVbase

0.39

42

0.434

1,860

0.68

  

Finns

[63]

0.45

400

0.434

1,860

0.60

LEPR

18

English males

HGVbase

0.27

322

0.290

1,839

0.41

  

Caucasiansc

[64]

0.28

56

0.290

1,839

0.98

  

Swedish males

[65]

0.24

284

0.290

1,839

0.09

 

19

Swedish males

[65]

0.15

284

0.182

1,776

0.21

 

20

Caucasiansc

[64]

0.38

56

0.353

1,860

0.79

  

Caucasiansc

dbSNP

0.4

42

0.353

1,860

0.64

  

English males

HGVbase

0.36

322

0.353

1,860

0.77

TGF-ß1

26

Caucasiansc

dbSNP

0.43

31

0.311

1,840

0.21

  

Caucasiansc

HGVbase

0.26

42

0.311

1,840

0.59

 

27

Caucasiansc

[66]

0.02

304

0.021

1,863

0.98

 

28

Danes

[66]

0.027

302

0.008

190

0.33

 

29

Caucasianc female DZ twins

[67]

0.25

1,802

0.274

1,852

0.08

TNFR2

31

UK Caucasians

[68]

0.23

192

0.198

1,842

0.39

  

Germans

[69]

0.25

94

0.198

1,842

0.33

  

Australians

HGVbase

0.26

197

0.198

1,842

0.05

UCP3

32

American Caucasians

[70]

0.21

56

0.265

1,767

0.49

  

Danes

[71]

0.27

857

0.265

1,767

0.85

  

French

[72]

0.22

894

0.265

1,767

0.01

 

33

Caucasiansc

[73]

0.01

165

0.000

295

0.44

 

34

American Caucasians

[70]

0.2

58

0.258

1,862

0.38

 

35

Caucasiansc

[74]

0.5

501

0.447

1,863

0.04

 

36

Caucasiansc

[73]

0.02

165

0.000

295

0.05

VDR

38

American Caucasians

[75]

0.42

49

0.373

1,861

0.61

  

English

[76]

0.4

241

0.373

1,861

0.47

  

Australians

[77]

0.35

43

0.373

1,861

0.87

 

40

Caucasiansc

dbSNP

0.42

107

0.419

1,860

0.94

  

English females

[76]

0.44

241

0.419

1,860

0.61

  

Australian males

[77]

0.47

39

0.419

1,860

0.66

  

Swiss

[78]

0.39

197

0.419

1,860

0.49

  

French infants

[79]

0.38

589

0.419

1,860

0.07

 

41

Caucasiansc

dbSNP

0.48

31

0.408

1,859

0.51

  

French

[80]

0.35

99

0.408

1,859

0.33

  

Australians

[81]

0.41

68

0.408

1,859

0.94

  1. For gene abbreviations and SNP designations see Table 1. a Present study. b Frequency of the allele corresponding to a minor allele in the present study. c Caucasians with unidentified ethnic background.