BDgene

SNP Report

Basic Info
Name rs2535629 dbSNP Ensembl
Location chr3:52799203 - 52799203(1)
Variant Alleles G/A
Ancestral Allele A
Minor Allele A
Minor Allele Frequence 0.484425
Functional Annotation downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant.
Consequence to Transcript downstream_gene_variant(ENST00000467268); intron_variant(ENST00000416872, ENST00000449956, ENST00000463893, ENST00000465243, ENST00000621946); non_coding_transcript_variant(ENST00000463893, ENST00000465243); upstream_gene_variant(ENST00000464804, ENST00000465314, ENST00000475931, ENST00000495622)
No. of Studies 3 (Positive: 3; Negative: 0; 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
Andreassen OA, 2013 Conditional FDR; BD loci given SCZ: P-value=0.0000129, FDR=0...... Conditional FDR; BD loci given SCZ: P-value=0.0000129, FDR=0.17896, FDR=0.00279 for BD and SCZ More... This SNP is with conditional FDR<0.05 in schizophrenia given...... This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. More... Positive
Major Depressive Disorder Working Group of the Psychiatric, G. C., 2013 P-value=0.000000362, OR=0.8687 for BIP, P-value=0.0000000058...... P-value=0.000000362, OR=0.8687 for BIP, P-value=0.000000005883, OR=0.8998 for combined sample More... In the combined analysis of these 819 SNPs, 15 exceeded geno...... In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.1. More... Positive
Cross-Disorder Group of the Psychiatric Genomics Consortium,2013 G/A Association analysis:P-value = 0.00000000000254,OR(95%CI) = ...... Association analysis:P-value = 0.00000000000254,OR(95%CI) = 1.1(1.07–1.12) when five disorders were combined More... Significant association was observed in cross-disorder analy...... Significant association was observed in cross-disorder analysis. More... Positive

SNP related genes (count: 1)
Approved Symbol Approved Name Location No. of Studies (Positive/Negative/Trend)
ITIH3 inter-alpha-trypsin inhibitor heavy chain 3 3p21.1 3(3/0/0)

SNPs in LD with rs2535629 (count: 9) View in gBrowse (chr3:52789432..52799203 )
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: 9)


Overlap with SZ from cross-disorder studies (count: 2)
Reference Statistical Result Description Result Category
Cross-Disorder Group of the Psychiatric Genomics Consortium,2013 Association analysis:P-value = 0.00000000000254,OR(95%CI) = 1.1(1.07–1.12) when five disorders were combined Significant association was observed in cross-disorder analysis. Positive
Andreassen OA, 2013 Conditional FDR; BD loci given SCZ: FDR=0.00279 for BD and SCZ This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. Positive

Overlap with MDD from cross-disorder studies (count: 2)
Reference Statistical Result Description Result Category
Cross-Disorder Group of the Psychiatric Genomics Consortium,2013 Association analysis:P-value = 0.00000000000254,OR(95%CI) = 1.1(1.07–1.12) when five disorders were combined Significant association was observed in cross-disorder analysis. Positive
Major Depressive Disorder Working Group of the Psychiatric, G. C., 2013 P-value=0.0009575, OR=0.9239 for MDD, P-value=0.000000005883, OR=0.8998 for combined sample In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.1. Positive

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