BDgene

SNP Report

Basic Info
Name rs3736544 dbSNP Ensembl
Location chr4:55443825 - 55443825(1)
Variant Alleles A/G
Ancestral Allele G
Minor Allele A
Minor Allele Frequence 0.276957
Functional Annotation intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant; upstream_gene_variant.
Consequence to Transcript intron_variant(ENST00000506103, ENST00000608091); NMD_transcript_variant(ENST00000506103); non_coding_transcript_exon_variant(ENST00000511124); non_coding_transcript_variant(ENST00000511124); synonymous_variant(ENST00000309964, ENST00000381322, ENST00000513440); upstream_gene_variant(ENST00000479384)
No. of Studies 3 (Positive: 1; Negative: 2; Trend: 0)
Source Literature
Overlap with SZ? YES
Overlap with MDD? YES

SNP related studies (count: 3)
Reference Allele Change Risk Allele Statistical Values Author Comments Result Category
Kripke, D. F.,2009 A/G TDT: In BP: OR=0.818, CHISQ=5.11, P-value = 0.0238, empirica...... TDT: In BP: OR=0.818, CHISQ=5.11, P-value = 0.0238, empirical P-value = 0.0241, corrected empirical P-value = 0.9728 More... Significant association was observed in the BP group. Significant association was observed in the BP group. Positive
Kishi, T.,2011(c) G>T For BD: Allele G, unadjusted analyses, OR=0.937, 95%CI=0.799...... For BD: Allele G, unadjusted analyses, OR=0.937, 95%CI=0.799-1.10, P-value = 0.426; adjusted analyses, OR=0.93, 95%CI=0.792-1.09, P-value = 0.37. Recessive: genotype GG and GT, unadjusted analyses, OR=0.77, 95%CI=0.500-1.17, P-value = 0.23; adjusted analyses, OR=0.762, 95%CI=0.491-1.17, P-value = 0.22 .Dominant: genotype GG, unadjusted analyses, OR=0.96, 95%CI=0.792-1.16, P-value = 0.675; adjusted analyses, OR=1, 95%CI=0.825-1.21, P-value = 0.989. Co-dominant: genotype GG, unadjusted analyses, OR=0.834, 95%CI=0.594-1.17, P-value = 0.293; adjusted analyses, OR=0.864, 95%CI=0.612-1.22, P-value = 0.404; Co-dominant: genotype GT, unadjusted analyses, OR=0.847, 95%CI=0.590-1.21, P-value = 0.365; adjusted analyses, OR=0.799, 95%CI=0.554-1.15, P-value = 0.227 More... No significant association was observed. No significant association was observed. Negative
Kishi, T.,2009(a) G/A chi-square test: 1. total samples: P-value = 0.663(Genotype)...... chi-square test: 1. total samples: P-value = 0.663(Genotype), P-value = 0.875(Allele) in BP 2. male samples: P-value = 0.485(Genotype), P-value = 0.773(Allele) in BP 3. female samples: P-value = 0.995(Genotype), P-value = 0.992(Allele) in BP More... No significant association was observed No significant association was observed Negative

SNP related genes (count: 2)
Approved Symbol Approved Name Location No. of Studies (Positive/Negative/Trend)
TMEM165 transmembrane protein 165 4q12 Mapped by Literature SNP
CLOCK clock circadian regulator 4q12 12(5/7/0)

SNPs in LD with rs3736544 (count: 53) View in gBrowse (chr4:55371160..55643126 )
The LD data used here is based on HapMap rel#27. LD SNP pairs were selected with a threshold r2<=0.8.

Literature-origin SNPs (count: 0)

LD-proxies (count: 53)


Overlap with SZ from cross-disorder studies (count: 1)
Reference Statistical Result Description Result Category
Kishi, T.,2009(a) chi-square test: 1. total samples: P-value = 0.296(Genotype), P-value = 0.317(Allele) in SCZ 2. male samples: P-value = 0.830(Genotype), P-value = 0.985(Allele) in SCZ 3. female samples: P-value = 0.218(Genotype), P-value = 0.191(Allele) in SCZ We did not find an association between these tag SNPs and Japanese schizophrenia, BP or MDD in any of the analyses. Negative

Overlap with MDD from cross-disorder studies (count: 2)
Reference Statistical Result Description Result Category
Kishi, T.,2011(c) For MDD:Allele G, unadjusted analyses, OR=0.783, 95%CI=0.585-1.05, P-value = 0.0989;adjusted analyses, OR=0.787, 95%CI=0.588-1.05, P-value = 0.106. Recessive:genotype GG and GT, unadjusted analyses, OR=2.19, 95%CI=1.10-4.10, P-value = 0.0187(0.224);adjusted analyses, OR=2.23, 95%CI=1.11-4.20, P-value = 0.0174(0.209) .Dominant:genotype GG, unadjusted analyses, OR=1.18, 95%CI=0.818-1.69, P-value = 0.372;adjusted analyses, OR=1.12, 95%CI=0.774-1.60, P-value = 0.551. Co-dominant:genotype GG, unadjusted analyses, OR=1.75, 95%CI=0.986-3.04, P-value = 0.0506;adjusted analyses, OR=1.67, 95%CI=0.939-2.92, P-value = 0.074;Co-dominant:genotype GT, unadjusted analyses, OR=0.161, 95%CI=0.873-2.96, P-value = 0.123;adjusted analyses, OR=1.74, 95%CI=0.940-3.21, P-value = 0.0751 Significant association was observed in recessive model , but this significance did not survive Bonferroni correction. Positive
Kishi, T.,2009(a) chi-square test: 1. total samples: P-value = 0.914(Genotype), P-value = 0.334(Allele) in MDD 2. male samples: P-value = 0.160(Genotype), P-value = 0.229(Allele) in MDD 3. female samples: P-value = 0.233(Genotype), P-value = 0.316(Allele) in MDD We did not find an association between these tag SNPs and Japanese schizophrenia, BP or MDD in any of the analyses. Negative

Copyright: Bioinformatics Lab, Institute of Psychology, Chinese Academy of Sciences Feedback Acknowledgements
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Last update: March 31, 2016