SNP Report

Basic Info

Name	rs9834970 dbSNP Ensembl
Location	chr3:36814539 - 36814539(1)
Variant Alleles	T/C
Ancestral Allele	T
Minor Allele	C
Minor Allele Frequence	0.481629
Functional Annotation	downstream_gene_variant.
Consequence to Transcript	downstream_gene_variant(ENST00000623312)
No. of Studies	6 (Positive: 3; Negative: 1; Trend: 2)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 6)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Green, E. K.,2012	T/C		BD ImmunoChip:P-value = 0.0519,OR = 0.91;ImmunoChip, PGC-BD ...... BD ImmunoChip:P-value = 0.0519,OR = 0.91;ImmunoChip, PGC-BD combined data:P-balue = 0.00000304,OR = 0.901 More...	Suggestive association was found. Suggestive association was found.	Trend
Ruderfer, D. M., 2013			P-value=3.90E-07 for BP, P-value=1.38E-10 for BP+SZ, Het P-v...... P-value=3.90E-07 for BP, P-value=1.38E-10 for BP+SZ, Het P-value=0.55 More...	Most significant SNP in six genome-wide significant regions....... Most significant SNP in six genome-wide significant regions. More...	Negative
Andreassen OA, 2013	C/T		Conditional FDR; BD loci given SCZ: P-value=0.00052, FDR=0.5...... Conditional FDR; BD loci given SCZ: P-value=0.00052, FDR=0.57626, FDR=0.02711 for BD and SCZ\|\|Conjunction FDR; pleiotropic loci in SCZ and BD: FDR=0.027 for BD and SZ, Z-score=3.47 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
Muhleisen, T. W., 2014	C/T	C	MooDS: P-value=0.0014, OR=1.15; PGC: P-value=6.19E-6, OR=1.1...... MooDS: P-value=0.0014, OR=1.15; PGC: P-value=6.19E-6, OR=1.11; MooDS-PGC: P-value=3.67E-8, adjusted P-value=4.81E-8, OR=1.12 More...	Eighteen GWAS SNPs showing genome-wide evidence for associat...... Eighteen GWAS SNPs showing genome-wide evidence for association with BD in the combined MooDS and PGC samples. More...	Positive
Chen, D. T.,2011		C	Meta-analysis results by ancestry: European and Asian-ancest...... Meta-analysis results by ancestry: European and Asian-ancestry phase I samples: Fixed effects P-value = 2.41EC11, Random effects P-value = 3.03EC13, I²=23.98, Q test=3.95, Q test P-value = 0.267; European and Asian-ancestry phase I & phase II samples: Fixed effects P-value = 4.71EC10, Random effects P-value = 1.48EC12, I²=54.34, Q test=10.95, Q test P-value = 0.052; European-ancestry phase I samples: Fixed effects P-value = 5.65EC10, Random effects P-value = 8.03EC12, I²=48.59, Q test=3.89, Q test P-value = 0.143; European-ancestry phase I and phase II samples: Fixed effects P-value = 1.03E-08, Random effects P-value = 3.08EC11, I²=63.4, Q test=10.93, Q test P-value = 0.027 More...	The results suggest novel association findings. The results suggest novel association findings.	Positive
Goes, F. S.,2012		T	OR = 0.82,P-value(Meta) = 0.0000000971 OR = 0.82,P-value(Meta) = 0.0000000971	Suggestive association was found. Suggestive association was found.	Trend

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
LRBA	LPS-responsive vesicle trafficking, beach and anchor containing	4q13	1(0/0/1)
TRANK1	tetratricopeptide repeat and ankyrin repeat containing 1	3p22.2	5(2/1/2)

SNPs in LD with rs9834970 (count: 4) View in gBrowse (chr3:36814539..36828739 )

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: 4)

rs_ID	Functional Annotation	r²[population]
rs1553656	downstream_gene_variant	0.801[CHD]; 0.884[JPT]
rs4789	3_prime_UTR_variant; upstream_gene_variant	0.945[JPT]
rs11129735	intron_variant; upstream_gene_variant	0.943[JPT]
rs4072458	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.89[JPT]

Overlap with SZ from cross-disorder studies (count: 2)

Reference	Statistical Result	Description	Result Category
Ruderfer, D. M., 2013	P-value=7.18E-05 for BP, P-value=5.53E-13 for BP+SZ, Het P-value=0.85	Most significant SNP in six genome-wide significant regions.	Negative
Andreassen OA, 2013	Conditional FDR; BD loci given SCZ: FDR=0.02711 for BD and SCZ\|\|Conjunction FDR; pleiotropic loci in SCZ and BD: FDR=0.027 for BD and SZ, Z-score=3.965 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)