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Table 5 Comparison of SNP allele frequencies of the studied Caucasian sample with the data on Asian populations 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 P
     Frequencyb n Frequency n  
ER-α 9 Japanese [83] 0.412 200 0.484 1,861 0.06
   Thai females [84] 0.337 129 0.484 1,861 <0.01
  10 Korean males [85] 0.39 219 0.449 1,861 0.11
   Korean females [86] 0.415 248 0.449 1,861 0.35
   Japanese children [87] 0.431 102 0.449 1,861 0.80
   Taiwanese [88] 0.39 246 0.449 1,861 0.09
   Thai females [89] 0.414 134 0.449 1,861 0.49
  11 SANGER 12 DNAs of Asian origin dbSNP 0.36 12 0.257 1,857 0.49
  12 Japanese [83] 0.483 200 0.218 1,859 <0.01
   Japanese females [90] 0.481 306 0.218 1,859 <0.01
  13 Japanese JSNP 0.34 744 0.098 1,863 <0.01
   TSC panel of unrelated Asians TSC 0.27 32 0.098 1,863 0.01
  14 Japanese JSNP 0.296 752 0.119 1,861 <0.01
  15 Japanese JSNP 0.18 741 0.203 1,863 0.21
   Japanese [83] 0.21 200 0.203 1,863 0.88
IL-6 16 Chinese [31] 0.997 147 0.434 1,860 <0.01
   Chinese males [31] 0.998 259 0.434 1,860 <0.01
   Japanese [31] 1.000 388 0.434 1,860 <0.01
LEPR 20 TSC panel of unrelated Asians dbSNP 0.13 42 0.353 1,860 <0.01
   Japanese JSNP 0.15 748 0.353 1,860 <0.01
PTHR1 22 Japanese JSNP 0.43 747 0.398 1,861 0.14
  23 Japanese JSNP 0.43 748 0.374 1,863 0.01
  24 Japanese JSNP 0.44 750 0.397 1,855 0.05
  25 Japanese JSNP 0.43 746 0.380 1,851 0.02
TGF-ß1 26 TSC panel of unrelated Asians dbSNP 0.47 36 0.311 1,840 0.06
TNFR2 31 Japanese [91] 0.113 265 0.198 1,842 <0.01
   Thai [92] 0.127 201 0.198 1,842 0.02
UCP3 33 Asiansc [73] 0.00 11 0.000 295 10.00
  35 Japanese JSNP 0.45 750 0.447 1,863 0.92
  36 Asiansc [73] 0.04 11 0.000 295 0.54
VDR 37 Japanese JSNP 0.23 750 0.281 1,861 0.01
  38 Japanese [93] 0.37 195 0.373 1,861 0.99
  40 SANGER 12 DNAs of Asian origin dbSNP 0.41 12 0.419 1,860 0.77
   Chinese females (Han nationality) [94] 0.043 162 0.419 1,860 <0.01
   Taiwanese [95] 0.083 90 0.419 1,860 <0.01
   Japanese [93] 0.13 195 0.419 1,860 0.02
   Koreans [96] 0.055 211 0.419 1,860 <0.01
   Thai females [97] 0.107 84 0.419 1,860 0.01
  41 Chinese (Han nationality) [98] 0.05 223 0.408 1,859 <0.01
   Japanese females [99] 0.135 119 0.408 1,859 <0.01
   Koreans [96] 0.055 120 0.408 1,859 <0.01
  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 Asians with unidentified ethnic background.