BDgene

SNP Report

Basic Info
Name rs1801260 dbSNP Ensembl
Location chr4:55435202 - 55435202(1)
Variant Alleles A/G
Ancestral Allele A
Minor Allele G
Minor Allele Frequence 0.229633
Functional Annotation 3_prime_UTR_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant.
Consequence to Transcript 3_prime_UTR_variant(ENST00000309964, ENST00000381322, ENST00000513440); intron_variant(ENST00000506103, ENST00000608091); NMD_transcript_variant(ENST00000506103); non_coding_transcript_exon_variant(ENST00000511124); non_coding_transcript_variant(ENST00000511124)
No. of Studies 6 (Positive: 3; Negative: 3; Trend: 0)
Source Literature
Overlap with SZ? YES
Overlap with MDD? YES

SNP related studies (count: 6)
Reference Allele Change Risk Allele Statistical Values Author Comments Result Category
Soria, V.,2010 X2-tests: allele P-value = 0.97, Model Codominant...... X2-tests: allele P-value = 0.97, Model Codominant, genotype P-value = 0.004, OR(95%CI)=0.61 (0.42-0.90) More... Significant association was found in BD. Significant association was found in BD. Positive
Yosifova, A.,2009 A/G Allelic association: P-value = 0.47 Allelic association: P-value = 0.47 No significant association was observed No significant association was observed Negative
Kishi, T.,2011(c) T>C For BD: Allele T, unadjusted analyses, OR=1.05, 95%CI=0.878-...... For BD: Allele T, unadjusted analyses, OR=1.05, 95%CI=0.878-1.26, P-value = 0.589; adjusted analyses, OR=1.06, 95%CI=0.889-1.27, P-value = 0.498. Recessive: genotype TT and TC, unadjusted analyses, OR=1.13, 95%CI=0.662-1.94, P-value = 0.654; adjusted analyses, OR=1.16, 95%CI=0.678-1.98, P-value = 0.596 .Dominant: genotype TT, unadjusted analyses, OR=1.05, 95%CI=0.853-1.29, P-value = 0.655; adjusted analyses, OR=1.07, 95%CI=0.866-1.31, P-value = 0.546. Co-dominant: genotype TT, unadjusted analyses, OR=1.12, 95%CI=0.750-1.67, P-value = 0.582; adjusted analyses, OR=1.15, 95%CI=0.771-1.72, P-value = 0.492; Co-dominant: genotype TC, unadjusted analyses, OR=1.04, 95%CI=0.675-1.61, P-value = 0.859; adjusted analyses, OR=1.04, 95%CI=0.671-1.61, P-value = 0.871 More... No significant association was observed. No significant association was observed. Negative
Kishi, T.,2009(a) T/C chi-square test: 1. total samples: P-value = 0.887(Genotype)...... chi-square test: 1. total samples: P-value = 0.887(Genotype), P-value = 0.976(Allele) in BP 2. male samples: P-value = 0.958(Genotype), P-value = 0.817(Allele) in BP 3. female samples: P-value = 0.888(Genotype), P-value = 0.885(Allele) in BP More... No significant association was observed No significant association was observed Negative
Dmitrzak-Weglarz, M. P., 2014 T/C BPDII: P-value=0.0138, FDR=0.1051, OR=1.45, 95%CI=1.08-1.95. BPDII: P-value=0.0138, FDR=0.1051, OR=1.45, 95%CI=1.08-1.95. SNPs rs1801260 of CLOCK gene was associated with BPDII risk. SNPs rs1801260 of CLOCK gene was associated with BPDII risk. Positive
Lee, K. Y.,2010 T/C C Association analysis: allele P-value = 0.012, genotype P-val...... Association analysis: allele P-value = 0.012, genotype P-value = 0.033, OR=1.61 (95% CI, 1.11-2.34). More... Significant association was found in BD. Significant association was found in BD. Positive

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 rs1801260 (count: 61) View in gBrowse (chr4:55369425..55616583 )
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: 61)


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 = 0.321(Genotype), P-value = 0.519(Allele) in SCZ 2. male samples: P-value = 0.856(Genotype), P-value = 0.680(Allele) in SCZ 3. female samples: P-value = 0.196(Genotype), P-value = 0.105(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: 3)
Reference Statistical Result Description Result Category
Kishi, T.,2011(c) For MDD:Allele T, unadjusted analyses, OR=1.12, 95%CI=0.790-1.59, P-value = 0.519;adjusted analyses, OR=1.13, 95%CI=0.785-1.59, P-value = 0.542. Recessive:genotype TT and TC, unadjusted analyses, OR=1.07, 95%CI=0.359-2.57, P-value = 0.893;adjusted analyses, OR=1.08, 95%CI=0.364-2.62, P-value = 0.87 .Dominant:genotype TT, unadjusted analyses, OR=0.85, 95%CI=0.562-1.26, P-value = 0.428;adjusted analyses, OR=0.847, 95%CI=0.560-1.26, P-value = 0.422. Co-dominant:genotype TT, unadjusted analyses, OR=0.898, 95%CI=0.401-1.78, P-value = 0.761;adjusted analyses, OR=0.898, 95%CI=0.403-1.79, P-value = 0.773;Co-dominant:genotype TC, unadjusted analyses, OR=1.3, 95%CI=0.550-2.86, P-value = 0.525;adjusted analyses, OR=1.32, 95%CI=0.557-2.91, P-value = 0.504 No significant association was observed. Negative
Kishi, T.,2009(a) chi-square test: 1. total samples:P-value = 0.833(Genotype), P-value = 0.972(Allele) in MDD 2. male samples: P-value = 0.451(Genotype), P-value = 0.746(Allele) in MDD 3. female samples: P-value = 0.648(Genotype), P-value = 0.872(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
Soria, V.,2010 X2-tests:allele P-value > 0.05, genotype P-value > 0.05 in all model No significant association was observed. Negative

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