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. Author manuscript; available in PMC: 2012 Dec 24.
Published in final edited form as: Biol Psychiatry. 2012 Aug 9;72(8):620–628. doi: 10.1016/j.biopsych.2012.05.035

Table 1.

Loci with Evidence for Association with Schizophrenia Identified in this Study

Chromosome rsID Positiona Candidate
Locus		 Discovery p Value
SGENE+		 p Value PGC p Value
Immunochip		 p Value
Combined
Risk
Allele		 RAF
Cases		 RAF
Control		 p Value
Discovery		 OR (95% CI)
1p21 rs987913b 95678503     — C .405 .357 2.92 × 10−5 1.24 (1.12–1.37)     NA   .0176       NA 1.48 × 10−4
3p14 rs862689a 71744029     — G .412 .364 2.68 × 10−5 1.24 (1.12–1.37)     NA   .0149   .312e 2.69 × 10−4
3p14 rs2684380b 71745822 FOXP1 T .427 .383 1.91 × 10−4 1.20 (1.09–1.33)     NA   .0332       NA 6.05 × 10−4
3q13 rs7618341 119268497     — A .599 .552 1.17 × 10−4 1.20 (1.10–1.32) .437 (−)   .0536   .0196 2.65 × 10−4
6p21 rs2523722 30273252 MHC G .778 .737 8.71 × 10−5 1.25 (1.12–1.39) .736 8.74 × 10−9 6.08 × 10−7 1.47 × 10−16
6p21 rs204999 32217957 MHC T .695 .631 2.77 × 10−8 1.33 (1.20–1.47) .621   .0442 1.93 × 10−7 5.37 × 10−10
6p21 rs7746922 32538953 MHC G .765 .723 1.30 × 10−4 1.23 (1.10–1.36) .197 2.82 × 10−5   .0314 4.48 × 10−9
7q31 rs4730488 110953401 IMMP2L C .517 .466 2.85 × 10−5 1.22 (1.11–1.34) .0718   .0287   .152 2.09 × 10−5
15q15 rs12595425b,c 38350279 PAK6 G .884 .852 8.26 × 10−6 1.44 (1.23–1.68)     NA   .0116       NA 2.74 × 10−5
22q13 rs9611198b 38285819 CACNA1I C .508 .458 4.35 × 10−5 1.22 (1.11–1.34)     NA 2.48 × 10−3       NA 7.56 × 10−6
22q13 rs9607658d 38287686 CACNA1I C .513 .463 5.60 × 10−5 1.21 (1.10–1.33) .275 (−) 7.19 × 10−3 6.33 × 10−3 1.11 × 10−5

The discovery, replication, and fixed effects meta-analysis results at SNPs for which there is evidence (one-sided p < .05) in the majority of the replication cohorts where data are available. All p values shown are two-sided, and (−) denotes that the direction of effect is opposite to that in the discovery analysis.

CI, confidence interval; NA, no data available; OR, odds ratio; PGC, Psychiatric GWAS Consortium; RAF, risk allele frequency; SNP, single nucleotide polymorphism.

a

National Center for Biotechnology Information human genome build 36 coordinates.

b

1000 Genomes imputed SNP.

c

SNP (rs12595425) not present in the replication data so replication measured at rs3784396 (R2 = .99).

d

HapMap imputed SNP.

e

Replication was attempted at a tag SNP in the Immunochip replication, rs2594113 (R2 = .97).