BDgene

SNP Report

Basic Info
Name rs9371601 dbSNP Ensembl
Location chr6:152469438 - 152469438(1)
Variant Alleles G/T
Ancestral Allele T
Minor Allele G
Minor Allele Frequence 0.440096
Functional Annotation intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant.
Consequence to Transcript intron_variant(ENST00000341594, ENST00000367248, ENST00000367253, ENST00000367255, ENST00000413186, ENST00000423061, ENST00000461872, ENST00000466159, ENST00000468937, ENST00000474655, ENST00000481502, ENST00000495090, ENST00000535896, ENST00000537750); NMD_transcript_variant(ENST00000474655); non_coding_transcript_variant(ENST00000461872, ENST00000468937, ENST00000481502, ENST00000535896); upstream_gene_variant(ENST00000498751)
No. of Studies 5 (Positive: 4; Negative: 0; Trend: 1)
Source Literature
Overlap with SZ? YES
Overlap with MDD? YES

SNP related studies (count: 5)
Reference Allele Change Risk Allele Statistical Values Author Comments Result Category
Green EK, 2013 T/G Association analysis: Independent BD sample, genotype trend ...... Association analysis: Independent BD sample, genotype trend P-value = 0.0095, allele OR (95% CI)=1.148 (1.03--1.27); BD-PGC combined analysis data, P-value = 6.71E-07, OR=1.099; Independent BD and BD-PGC combined data, P-value = 2.9E-08, OR=1.104 More... Significant association was observed in BD. Significant association was observed in BD. Positive
Green, E. K.,2012 G/T BD ImmunoChip:P-value = 0.0764,OR = 0.916;ImmunoChip, PGC-BD...... BD ImmunoChip:P-value = 0.0764,OR = 0.916;ImmunoChip, PGC-BD combined data:P-balue = 0.000000138,OR = 0.911 More... Suggestive association was found. Suggestive association was found. Trend
Andreassen OA, 2013 Conditional FDR; BD loci given SCZ: P-value=0.0000011, FDR=0...... Conditional FDR; BD loci given SCZ: P-value=0.0000011, FDR=0.06351, FDR=0.02196 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
Cross-Disorder Group of the Psychiatric Genomics Consortium,2013 T/G Association analysis:P-value = 0.00000000427 in BPD. Association analysis:P-value = 0.00000000427 in BPD. Significant association was observed in BPD. Significant association was observed in BPD. Positive
Sklar, P.,2011 T/G genome-wide association: allele, OR(95%CI)=(1.21-1.10), P-va...... genome-wide association: allele, OR(95%CI)=(1.21-1.10), P-value(raw)=4.3E-09, P-value(GC)=4.3E-08 for primary analysis More... Significant association was found . Significant association was found . Positive

SNP related genes (count: 1)
Approved Symbol Approved Name Location No. of Studies (Positive/Negative/Trend)
SYNE1 spectrin repeat containing, nuclear envelope 1 6q25.2 6(3/2/1)

SNPs in LD with rs9371601 (count: 63) View in gBrowse (chr6:152389729..152513359 )
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: 63)


Overlap with SZ from cross-disorder studies (count: 1)
Reference Statistical Result Description Result Category
Andreassen OA, 2013 Conditional FDR; BD loci given SCZ: FDR=0.02196 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: 1)
Reference Statistical Result Description Result Category
Green EK, 2013 Association analysis:genotype trend P-value = 0.063, allele OR (95% CI)=1.111 (0.99--1.24) with independent control;genotype trend P-value = 0.032, allele OR (95% CI)=1.118 (1.01--1.24) with all controls (WTCCC and independent) Significant association was observed in MDD. Positive