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. Author manuscript; available in PMC: 2011 Nov 28.
Published in final edited form as: J Psychiatr Res. 2010 Feb 24;44(12):748–753. doi: 10.1016/j.jpsychires.2010.02.002

Table 1.

The most significant association results from the combined analysis.

Discovery sample
Cases n = 201
Controls n = 307
 Replication sample
Cases n = 2663
Controls n = 13,780
 Combined analysis
Cases n = 2864
Controls n = 14,087
Chromosome Affy SNP Minor allele SZ CON Allelic (P) Odds ratio Illumina SNP R 2 CMH (P) Odds ratio Meta CMH (P) Locus
9 rs7045881 A 0.06 0.13 6.39E-04 0455 rs7035755 1 1.96E-04 0.86 2.12E-06 PLAA
16 rs433598 T 0.38 0.27 1.06E-04 1.7 rs433598 1 1.88E-03 1.13 3.27E-06 ACSM1
10 rs10761482 T 0.17 0.26 7.33E-04 0.58 rs4948410 0.83 6.75E-04 0.86 7.68E-06 ANK3
10 rs4313476 C 0.46 0.33 3.63E-05 1.72 rs4313476 1 3.59E-02 1.08 1.90E-05 GLUDP5
16 rs163274 C 0.35 0.24 3.66E-04 1.65 rs163234 0.96 4.72E-03 1.12 2.46E-05 ACSM1
15 rs951442 C 0.37 0.48 3.44E-04 0.63 rs951442 1 8.55E-03 0.91 4.04E-05 RYR3
6 rs9296494 C 0.24 0.35 4.40E-04 0.6 rs9296494 1 9.33E-03 0.9 5.50E-05 PHACTR1
20 rs4813250 T 0.33 0.45 9.53E-05 0.59 rs6080400 0.9 4.50E-02 0.93 5.72E-05 OTOR
20 rs6111277 A 0.33 0.45 1.07E-04 0.6 rs6080400 0.9 4.50E-02 0.93 6.37E-05 OTOR
16 rs163234 G 0.36 0.26 1.19E-03 1.58 rs163234 1 4.72E-03 1.12 7.36E-05 ACSM1
6 rs6911854 C 0.18 0.1 2.32E-04 1.97 rs9443543 0.8 2.73E-02 1.13 8.22E-05 AL591500.6>
16 rs12324972 T 0.3 0.21 7.84E-04 1.64 rs6497501 0.86 9.02E-03 1.12 9.09E-05 ACSM2
16 rs163275 G 0.33 0.24 1.53E-03 1.57 rs163234 0.96 4.72E-03 1.12 9.28E-05 ACSM1
3 rs2372342 C 0.09 0.04 3.06E-04 2.57 rs2372342 1 2.70E-02 1.04 1.05E-04 C3orf39|SNRK
8 rs10106755 A 0.28 0.38 1.01E-03 0.64 rs13273158 0.9 9.97E-03 0.9 1.26E-04 PSD3
6 rs946138 T 0.17 0.09 4.12E-04 1.95 rs9443543 0.86 2.73E-02 1.13 1.40E-04 AL591500.6>
6 rs3857446 C 0.18 0.11 4.97E-04 1.89 rs9443543 1 2.73E-02 1.13 1.66E-04 AL591500.6>
14 rs6573695 G 0.03 0.09 3.16E-04 0.34 rs1952070 1 4.58E-02 0.89 1.75E-04 GPHN
10 rs4316429 T 0.17 0.1 9.08E-04 1.88 rs7092779 0.92 2.61E-02 1.13 2.76E-04 PCDH15
18 rs4264496 A 0.4 0.5 1.54E-03 0.66 rs11662668 0.9 1.67E-02 1.09 2.98E-04 CTAGE1|RBBP8
6 rs2050689 T 0.17 0.1 1.01E-03 1.85 rs9443543 1 2.73E-02 1.13 3.18E-04 AL591500.6>
10 rs1539318 C 0.16 0.1 1.61E-03 1.83 rs7092779 0.92 2.61E-02 1.13 4.64E-04 PCDH15
14 rs17247749 C 0.04 0.1 9.48E-04 0.39 rs1952070 1 4.58E-02 0.89 4.79E-04 GPHN
14 rs6573719 G 0.04 0.09 9.95E-04 0.4 rs1952070 1 4.58E-02 0.89 5.01E-04 GPHN
14 rs17836572 C 0.04 0.09 1.04E-03 0.4 rs1952070 1 4.58E-02 0.89 5.23E-04 GPHN
14 rs1885198 T 0.04 0.09 1.04E-03 0.4 rs1952070 1 4.58E-02 0.89 5.23E-04 GPHN
14 rs6573706 T 0.04 0.09 1.04E-03 0.4 rs1952070 1 4.58E-02 0.89 5.23E-04 GPHN
14 rs7154017 C 0.04 0.09 1.04E-03 0.4 rs1952070 1 4.58E-02 0.89 5.23E-04 GPHN
14 rs7157740 G 0.04 0.09 1.04E-03 0.4 rs1952070 1 4.58E-02 0.89 5.23E-04 GPHN
11 rs500063 T 0.39 0.49 1.24E-03 0.66 rs500063 1 4.06E-02 0.92 5.48E-04 SLC35F2
14 rs9783601 G 0.04 0.09 1.12E-03 0.4 rs1952070 1 4.58E-02 0.89 5.57E-04 GPHN
20 rs6100223 C 0.18 0.27 1.27E-03 0.6 rs6015375 0.84 4.33E-02 0.92 5.95E-04 NPEPL1|GNAS

Note: Combined analysis of allelic association tests for SNPs with a nominal significant P value in the replication sample with concurring OR between the discovery and the replication sample. The minor allele frequencies are listed in SZ (cases) and CON (controls).