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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.