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Table 3 Hardy-Weinberg equilibrium (HWE) test and effect allele frequency (EAF) in Chinese children for32 GWA studies -derived SNPs

From: Association of common variants identified by recent genome-wide association studies with obesity in Chinese children: a case-control study

SNP Nearest gene Chr Position Allele HWE P-valuea EAFb EAFc F ST
Effect Other
Speliotes et al. 2010 (in children and adults of European ancestry) [4]
rs1558902 FTO 16 52361075 A T 0.58 0.13 0.42 0.105e
rs2867125 TMEM18 2 612827 C T 0.20 0.91 0.83 0.014
rs571312 MC4R 18 55990749 A C 0.67 0.23 0.24 0.000
rs10938397 GNPDA2 4 44877284 G A 0.54 0.31 0.43 0.015
rs10767664 BDNF 11 27682562 A T 0.30 0.55 0.78 0.059
rs2815752 NEGR1 1 72585028 A G 0.97 0.92 0.61 0.134e
rs7359397 SH2B1 16 28793160 T C 0.17 0.16 0.40 0.071
rs9816226 ETV5 3 187317193 T A 0.36 0.97 0.82 0.060
rs3817334 MTCH2 11 47607569 T C 0.16 0.33 0.41 0.007
rs29942d KCTD15 19 39001117 C T 0.76 0.25 0.31 0.004
rs543874 SEC16B 1 176156103 G A 0.80 0.22 0.19 0.001
rs987237 TFAP2B 6 50911009 G A 0.52 0.18 0.18 0.000
rs7138803 FAIM2 12 48533735 A G 0.01 0.28 0.38 0.011
rs713586 RBJ 2 25011512 C T 0.77 0.49 0.47 0.000
rs2241423 MAP2K5 15 65873892 G A 0.67 0.41 0.78 0.142e
rs2287019 QPCTL 19 50894012 C T 0.09 0.82 0.80 0.001
rs1514175 TNNI3K 1 74764232 A G 0.91 0.78 0.43 0.128e
rs2112347 FLJ35779 5 75050998 T G 0.88 0.44 0.63 0.036
rs16912921d LRRN6C 9 28403461 A C 0.19 0.30 0.34 0.002
rs3810291 TMEM160 19 52260843 A G 0.58 0.29 0.67 0.145e
rs1555543 PTBP2 1 96717385 C A 0.81 0.87 0.59 0.099
rs9579083d MTIF3 13 26915270 C G 0.87 0.15 0.23 0.010
rs4929949 RPL27A 11 8561169 C T 0.79 0.40 0.52 0.014
rs206936 NUDT3 6 34410847 G A 0.30 0.51 0.21 0.098
Scherag et al. 2010 (in children and adults of European ancestry) [6]
rs12145833 SDCCAG8 1 241550377 T G 0.55 0.91 0.87 0.004
rs13278851 TNKS/MSRA 8 9788282 A G 0.28 0.14 0.11 0.002
Bradfield et al. 2012 (in children of European ancestry) [5]
rs9568856 OLFM4 13 52962982 A G 0.34 0.33 0.16 0.039
rs9299 HOXB5 17 44024429 A G 0.44 0.53 0.65 0.015
Okada et al. 2012 (in East Asians) [7]
rs2206734 CDKAL1 6 20802863 G A 0.66 0.59 0.59 0.000
rs11142387 KLF9 9 72188152 C A 0.96 0.33 0.46 0.018
Wen et al. 2012 (in East Asians) [8]
rs261966d PCSK1 5 95875343 G A 0.53 0.45 0.42 0.001
rs12597579 GP2 16 20165368 C T 0.99 0.73 0.80 0.007
  1. Chr Chromosome; Position: NCBI build 36.3 (NCBI, Bethesda, MD); EAF Effect allele frequency, HWE Hardy-Weinberg equilibrium
  2. aHWE P-value in normal-weight Chinese children
  3. bEffect allele frequency in all genotyped individuals of the present study
  4. cEffect allele frequency of SNPs in the discovery studies (Ref. [4-8]), and that of each proxy SNP is from NCBI database among the same populations that in the discovery study
  5. dProxy SNPs were used in the present study to replace the SNPs from the discovery studies
  6. eFST > 0.10 as indicator of large genetic differentiation between population in the present study and that in the discovery study