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. Author manuscript; available in PMC: 2017 Feb 8.
Published in final edited form as: JAMA Psychiatry. 2013 Jun;70(6):573–581. doi: 10.1001/jamapsychiatry.2013.288

Table 1.

SNPs With P≤.005 in Combined Replication Analysis and Direction of Effect Identical to GWAS Meta-analysis

SNP Chr Coordinatea Allele Frequencyb
Oddsc
P Value
Reasong Directionh Genes
European Asian African European Asian African Replicationd Meta-analysise Overallf
rs2296268 1 36603165 T 0.29 0.56 0.68 1.1 1.2 1.0 3.30 × 10−3 7.02 × 10−3 3.21 × 10−5 1 + TRAPPC3
rs589249 1 37162352 G 0.64 0.45 0.17 1.2 1.1 1.2 3.08 × 10−3 2.17 × 10−5 3.48 × 10−7 3 + GRIK3i
rs4664494 2 152499580 T 0.82 0.55 0.42 1.2 1.1 1.2 1.57 × 10−3 6.93 × 10−2 2.87 × 10−4 1 + NEB
rs10193188 2 152551210 G 0.18 0.51 0.57 0.8 1.0 0.8 2.19 × 10−3 1.40 × 10−2 9.46 × 10−5 4 − NEB
rs6739563 2 201134216 T 0.84 0.80 0.87 1.2 1.2 1.0 3.23 × 10−3 2.44 × 10−2 2.38 × 10−4 2 + SPATS2Li
rs12496073 3 25033188 G 0.34 0.51 0.16 1.2 1.1 0.9 4.34 × 10−3 3.10 × 10−3 3.98 × 10−5 2 + j
rs6898746 5 60843706 T 0.51 0.28 0.88 0.8 1.0 0.8 2.78 × 10−3 3.72 × 10−3 3.10 × 10−5 2 − ZSWIM6i
rs2857605 6 31524851 G 0.81 0.86 0.93 1.4 1.0 1.2 3.34 × 10−3 8.78 × 10−1 2.90 × 10−2 4 + NFKBIL1
rs3130349 6 32147696 G 0.15 0.08 0.12 1.3 1.1 1.3 3.76 × 10−3 3.16 × 10−3 1.48 × 10−5 1 + RNF5
rs3132935 6 32171075 G 0.82 0.85 0.83 0.8 0.9 1.0 1.51 × 10−3 2.17 × 10−4 3.16 × 10−7 1 − NOTCH4
rs3132947 6 32176782 T 0.82 0.85 0.83 0.8 0.9 1.0 1.83 × 10−3 2.40 × 10−4 4.34 × 10−7 1 − NOTCH4
rs4409766 10 104616663 T 0.12 0.27 0.25 1.2 1.1 1.5 1.21 × 10−3 1.38 × 10−2 5.57 × 10−5 4 + C10orf32
rs3740390 10 104638480 G 0.11 0.26 0.07 1.3 1.1 1.6 7.90 × 10−4 3.30 × 10−4 9.01 × 10−7 3 + AS3MT
rs7897654 10 104662458 T 0.30 0.46 0.29 1.2 1.0 1.3 3.10 × 10−3 1.76 × 10−5 2.93 × 10−7 3 + AS3MTi
rs12221064 10 104677126 T 0.89 0.74 0.94 0.8 0.9 0.6 1.26 × 10−3 3.20 × 10−4 1.40 × 10−6 2 − CNNM2i
rs11191499 10 104764271 T 0.11 0.26 0.06 1.3 1.1 1.6 9.90 × 10−4 1.99 × 10−4 7.09 × 10−7 2 + CNNM2
rs11191514 10 104773364 T 0.89 0.74 0.94 0.8 0.9 0.6 9.83 × 10−4 1.70 × 10−4 6.07 × 10−7 3 − CNNM2
rs17094683 10 104851301 T 0.90 0.74 0.94 0.8 0.9 0.6 1.59 × 10−3 6.24 × 10−5 4.09 × 10−7 3 − NT5C2
rs1564483 18 60794654 G 0.25 0.34 0.13 1.2 1.1 1.2 2.75 × 10−3 4.69 × 10−3 1.69 × 10−5 1 + BCL2
rs12159787 22 40870699 G 0.91 0.81 0.78 0.8 0.9 0.9 4.07 × 10−3 8.45 × 10−3 9.89 × 10−5 2 − MKL1
rs5995871 22 40922332 G 0.91 0.81 0.94 0.8 0.9 0.9 4.94 × 10−3 1.16 × 10−2 8.36 × 10−5 1 − MKL1
rs6001980 22 41004384 T 0.09 0.19 0.07 1.3 1.1 1.2 4.96 × 10−3 3.60 × 10−3 5.22 × 10−5 2 + MKL1
rs138880 22 50218611 C 0.78 0.89 0.26 1.1 1.3 1.2 2.75 × 10−3 9.49 × 10−6 1.53 × 10−7 3 + BRD1i

Abbreviations: Chr, chromosome; GWAS, genome-wide association studies; SNP, single-nucleotide polymorphism.

a

Indicates location of chromosome in the human genome build 19.

b

Indicates frequency of allele in each ancestry group. Linkage disequilibrium between adjacent markers (r2>0.8) is indicated using boldface type.

c

Indicates the effect in each ancestry group.

d

Indicates combined results from families with European, Asian, and African ancestry.

e

Depending on why the SNP was selected, indicates with or without data integration.

f

Indicates the combined P value from replication and meta-analysis.

g

Indicates reason for selection as only after data integration (1), only because of top P value in GWAS meta-analysis (2), both (3), or other (4).

h

Indicates direction of effect in the replication and meta-analysis where the allele increases (plus sign) or decreases (minus sign) the risk.

i

Indicates SNP is located outside of gene boundaries, and the closest gene within 100 kilobases (kb) is given.

j

Indicates that the closest gene is located more than 100 kb from the SNP.