SNP Report

Basic Info

Name	rs3134942 dbSNP Ensembl
Location	chrCHR_HSCHR6_MHC_SSTO_CTG1:32208676 - 32208676(1)
Variant Alleles	G/T
Ancestral Allele	T
Minor Allele	T
Minor Allele Frequence	0.0776757
Functional Annotation	non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant; upstream_gene_variant.
Consequence to Transcript	non_coding_transcript_exon_variant(ENST00000474612); non_coding_transcript_variant(ENST00000474612); synonymous_variant(ENST00000375023); upstream_gene_variant(ENST00000491215, ENST00000466682, ENST00000466682, ENST00000425600, ENST00000487071, ENST00000485109, ENST00000485109, ENST00000437843, ENST00000470539, ENST00000471956, ENST00000471956, ENST00000454571, ENST00000474325, ENST00000465833, ENST00000465833, ENST00000439349, ENST00000474061, ENST00000476219, ENST00000476219, ENST00000383264, ENST00000468933, ENST00000495284, ENST00000495284, ENST00000457094, ENST00000497260)
No. of Studies	1 (Positive: 1; Negative: 0; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 1)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Andreassen OA, 2013	G/T		Conditional FDR; BD loci given SCZ: P-value=0.00115, FDR=0.6...... Conditional FDR; BD loci given SCZ: P-value=0.00115, FDR=0.66028, FDR=0.04844 for BD and SCZ\|\|Conjunction FDR; pleiotropic loci in SCZ and BD: FDR=0.048 for BD and SZ, Z-score=3.251 for BD 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'. This SNP is with conjunction FDR<0.08 with schizophrenia and bipolar disorder considered jointly. More...	Positive

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
NOTCH4	notch 4	6p21.3	2(0/2/0)

SNPs in LD with rs3134942 (count: 0) View in gBrowse (chrCHR_HSCHR6_MHC_SSTO_CTG1:32208676..32208676 )

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=0.04844 for BD and SCZ\|\|Conjunction FDR; pleiotropic loci in SCZ and BD: FDR=0.048 for BD and SZ, Z-score=3.571 for SZ	This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. This SNP is with conjunction FDR<0.08 with schizophrenia and bipolar disorder considered jointly.	Positive

Overlap with MDD from cross-disorder studies (count: 0)