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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 2.

Evidence in the Discovery Data at Loci Previously Reported to be Associated with Schizophrenia at p < 5 × 10−8

Chr rsID Positiona Locus of
Interest		 Risk
Allele		 Case
RAF		 Control
RAF		 p Valueb OR (95% CI) Reference
  1 rs1625579c 98275522 MIR137 T .83 .82   .035 1.12 (.99–1.27) (9)
  1 rs10489202 166169703     — A .25 .23   .027 1.11 (1.00–1.24) (10)
  2 rs2312147d 58076432 VRK2 C .64 .61 4.94 × 10−3 1.14 (1.03–1.25) (12)
  2 rs1344706e 185486673 ZNF804A T .65 .63 5.56 × 10−3 1.17 (1.01–1.23) (4)
  3 rs6782299e 182033396     — T .74 .73   .148 1.07 (.94–1.23) (3)
  6 rs1635d 28335583 NKAPL C .97 .97   .360 1.05 (.79–1.41) (11)
  6 rs2142731 28358892 PGBD1 C .003 .002   .099 1.92 (.71–5.18) (11)
  6 rs3131296d 32280971 MHC C .85 .82 1.88 × 10−4 1.26 (1.11–1.44) (12)
  6 rs9272219 32710247 MHC G .77 .74   .016 1.13 (1.01–1.26) (6)
  8 rs10503253c 4168252 CSMD1 A .22 .19 9.06 × 10−3 1.15 (1.02 × 1.30) (9)
  8 rs16887244 38150502     — A .77 .75   .084 1.08 (.97–1.21) (10)
  8 rs7004633c 89829427 MMP16 G .18 .16   .062 1.11 (.97–1.26) (9)
10 rs11191580c 104896201 NT5C2 T .93 .92   .139 1.10 (.92–1.32) (9)
11 rs835784 44820394 TSPAN18 T .48 .47   .256 1.03 (.94–1.14) (11)
11 rs12807809 124111495 NRGN T .83 .82   .144 1.07 (.94–1.22) (12)
18 rs17594526e 51209236 TCF4 A .03 .02 1.05 × 10−3 1.77 (1.22–2.54) (3)
18 rs9960767d 51306000 TCF4 C .05 .04   .080 1.18 (.94–1.49) (12)

Chr, chromosome; CI, confidence interval; GWAS, genome-wide association studies; ISC, International Schizophrenia Consortium; OR, odds ratio; PGC, Psychiatric GWAS Consortium; RAF, risk allele frequency, SCZ, schizophrenia; SNP, single nucleotide polymorphism; WTCCC2, Wellcome Trust Case Control Consortium 2.

a

National Center for Biotechnology Information human genome build 36 coordinates.

b

p value is one sided in the direction of risk in the original study; the direction of effect is the same as in the original study for all SNPs.

c

The WTCCC2-SCZ data contributed to the PGC GWAS meta-analysis.

d

SNP imputed in WTCCC2 data.

e

There was some overlap between the WTCCC2-SCZ sample and the O’Donovan et al. (4) and ISC studies. These cases and control subjects are excluded from the WTCCC2-SCZ sample for the purposes of the current analysis.