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Table 3 Top 20 SNPs and the landmark SNP2140 in Stage 1 allelic and genotypic association tests

From: Lack of association of genetic variation in chromosome region 15q14-22.1 with type 2 diabetes in a Japanese population

       Stage 1 Stage 2 Stage 1 + Stage 2
  SNP Marker rs# Gene symbol Position Allele 1/2 Allele 1 frequency case Allele 1 frequency control p value of allele frequency p value of genotype frequency p value of Armitage trend testa) Allele 1 frequency case Allele 1 frequency control p value of allele frequency p value of genotype frequency p value of Armitage trend testa) Allele 1 frequency case Allele 1 frequency control p value of allele frequency p value of genotype frequency p value of Armitage trend testa)
1 SNP2248 - ATP8B4 48175632 G/T 0.23 0.31 0.00053 0.0024 0.00052 0.29 0.28 0.59 0.61 0.59 0.27 0.30 0.075 0.19 0.075
2 SNP2372 rs4261468 RAB27A 53342894 A/G 0.49 0.41 0.00091 0.0034 0.00078 0.47 0.48 0.67 0.80 0.66 0.48 0.45 0.076 0.20 0.072
3 SNP3295 rs12443171 intergenic 48225107 C/T 0.34 0.43 0.00091 0.0030 0.00099 0.38 0.40 0.49 0.66 0.49 0.37 0.41 0.0079 0.018 0.0081
4 SNP3347 rs1386166 intergenic 51376772 A/G 0.35 0.44 0.0014 0.0013 0.0016 0.37 0.40 0.15 0.23 0.16 0.36 0.42 0.0017 0.0080 0.0021
5 SNP1439 rs9972478 RAB27A 53347024 A/C 0.30 0.23 0.0017 0.0068 0.0016 0.27 0.29 0.28 0.34 0.27 0.28 0.26 0.25 0.37 0.25
6 SNP3391 rs2414351 intergenic 52746565 C/G 0.24 0.18 0.0019 0.0066 0.0017 0.19 0.21 0.16 0.39 0.17 0.21 0.20 0.34 0.64 0.35
7 SNP2373 rs2305424 RAB27A 53368640 C/T 0.47 0.55 0.0037 0.011 0.0032 0.48 0.48 0.97 0.86 0.96 0.48 0.51 0.061 0.11 0.058
8 SNP1441 rs2414409 PIGB 53419009 C/T 0.47 0.55 0.0039 0.013 0.0034 0.48 0.48 0.93 0.91 0.93 0.48 0.51 0.077 0.16 0.074
9 SNP1280 rs2278167 SLC27A2 48285140 G/T 0.61 0.54 0.0050 0.014 0.0047 0.59 0.56 0.20 0.095 0.19 0.60 0.55 0.0054 0.013 0.0047
10 SNP2039 rs2412424 FSIP1 37765425 C/T 0.65 0.59 0.0075 0.022 0.0061 0.62 0.62 0.91 0.62 0.91 0.64 0.61 0.072 0.16 0.067
11 SNP2098 rs4924524 CHAC1 39042673 C/T 0.76 0.70 0.0060 0.022 0.0064 0.73 0.76 0.21 0.082 0.21 0.75 0.73 0.42 0.15 0.42
12 SNP1440 rs7183960 PIGB 53409987 C/T 0.47 0.54 0.0074 0.022 0.0067 0.48 0.48 0.80 0.93 0.79 0.48 0.50 0.13 0.26 0.13
13 SNP2249 rs11638841 ATP8B4 48203899 C/G 0.73 0.66 0.0062 0.026 0.0069 0.67 0.68 0.72 0.89 0.72 0.70 0.67 0.15 0.33 0.15
14 SNP3176 rs996215 intergenic 44577114 A/G 0.23 0.30 0.0067 0.027 0.0073 0.28 0.27 0.51 0.74 0.50 0.26 0.28 0.22 0.46 0.22
15 SNP2097 rs4924523 CHAC1 39042662 A/T 0.24 0.30 0.0072 0.025 0.0076 0.27 0.24 0.22 0.085 0.22 0.26 0.27 0.43 0.15 0.43
16 SNP2072 rs936216 PAK6 38344560 A/C 0.75 0.81 0.0092 0.0075 0.0084 0.75 0.78 0.093 0.14 0.10 0.75 0.79 0.0032 0.015 0.0038
17 SNP1438 rs12910930 RAB27A 53332998 C/G 0.33 0.27 0.0095 0.016 0.0084 0.28 0.31 0.20 0.25 0.20 0.30 0.29 0.49 0.24 0.49
18 SNP2041 rs2254829 FSIP1 37779957 C/T 0.66 0.59 0.0099 0.030 0.0085 0.63 0.62 0.84 0.67 0.84 0.64 0.61 0.071 0.17 0.068
19 SNP1444 rs3743203 CCPG1 53436254 C/T 0.47 0.53 0.010 0.037 0.010 0.47 0.47 0.98 0.83 0.98 0.47 0.49 0.11 0.22 0.10
20 SNP3096 rs156787 FLJ39531 37335619 A/G 0.18 0.23 0.0092 0.038 0.011 0.18 0.21 0.065 0.065 0.062 0.18 0.22 0.0020 0.0041 0.0022
* SNP2140 rs2412747 UBR1 41074095 C/T 0.81 0.77 0.049 0.11 0.049 0.79 0.75 0.039 0.072 0.039 0.80 0.76 0.0043 0.0081 0.0045
  1. Significant results (p < 0.05) and (*) SNP2140 (rs2412747) in the UBR1 are shown in bold type. a)Armitage trend test was performed by using the DeFinetti program http://ijg.gsf.de/cgi-bin/hw/hwal.pl. The positions of top 20 SNPs with their p values in the increasing order in Armitage trend test are almost the same as those in allelic test, except for SNP 2039, 1440, and 3096 of which p values were underlined.