SNP Report

Basic Info

Name	rs1341402 dbSNP Ensembl
Location	chr13:105463160 - 105463160(1)
Variant Alleles	T/C
Ancestral Allele	T
Minor Allele	C
Minor Allele Frequence	0.0742811
Functional Annotation	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant.
Consequence to Transcript	downstream_gene_variant(ENST00000610818, ENST00000613021); intron_variant(ENST00000448407); non_coding_transcript_variant(ENST00000448407); upstream_gene_variant(ENST00000329625, ENST00000375936, ENST00000471432, ENST00000473269, ENST00000488534, ENST00000489237, ENST00000559369, ENST00000595812, ENST00000600388, ENST00000601240, ENST00000618629)
No. of Studies	10 (Positive: 3; Negative: 7; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 10)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Schumacher, J.,2004	T/C		Association analysis: allele P-value = 0.437, OR=1.11, genot...... Association analysis: allele P-value = 0.437, OR=1.11, genotype P-value = 0.629, OR=1.17 More...	No significant association was observed in BD. No significant association was observed in BD.	Negative
Bass, N. J.,2009	C/T		chi-squared tests: for BP, allele, X²(1 d.f.)=0.1...... chi-squared tests: for BP, allele, X²(1 d.f.)=0.172, P-value = 0.679 More...	No significant association was observed. No significant association was observed.	Negative
Hattori, E.,2003	C/T	T	Association analysis: for CNG pedigrees, TDT P-value = 0.007...... Association analysis: for CNG pedigrees, TDT P-value = 0.0075, Transmission Ratio=0.8; for NIMH pedigrees, TDT P-value = 0.58, Transmission Ratio=0.56 More...	Significant association was found in BD. Significant association was found in BD.	Positive
Grigoroiu-Serbanescu, M.,2010	T/C		Allelic association analysis: for non-psychotic patients, P-...... Allelic association analysis: for non-psychotic patients, P-value = 0.294, OR(95%CI)=0.68(0.33-1.42); for psychotic patients, P-value = 0.934, OR(95%CI)=0.99(0.70-1.40) More...	No significant association was observed in BD. No significant association was observed in BD.	Negative
Muller, D. J.,2011	T/C		FBAT: for total sample, variance of the S-statistic=47.1, Z-...... FBAT: for total sample, variance of the S-statistic=47.1, Z-score=-0.63, P-value = 0.53; for European sample, variance of the S-statistic=45.6, Z-score=-0.49, P-value = 0.63; for BD patients with psychotic symptoms, variance of the S-statistic=24.3, Z-score=-0.31, P-value = 0.76; for BD patients without psychotic symptoms, variance of the S-statistic=15, Z-score=-0.52, P-value = 0.61 More...	No significant association was observed. No significant association was observed.	Negative
Schulze, T. G.,2005	G/A	G	For German group : All Patients With Bipolar Affective Disor...... For German group : All Patients With Bipolar Affective Disorder, P-value > 0.05 , OR=0.86, 95CI=0.91-1.47.Patients With a History of Psychotic Symptoms, P-value > 0.05 , OR=0.89, 95CI=0.68-1.19. Patients With No History of Psychotic Symptoms, P-value > 0.05 , OR=0.75, 95CI=0.52-1.08 More...	No significant association was observed. No significant association was observed.	Negative
Williams, N. M., 2006			allelic P-value = 0.03, Gene-wide test P-value = 0.045 in Bi...... allelic P-value = 0.03, Gene-wide test P-value = 0.045 in Bipolar I Disorder More...	We observed nominally significant evidence (P=.01-.047) for ...... We observed nominally significant evidence (P=.01-.047) for allelic association with 3 of the polymorphisms for bipolar disorder and significant evidence for whole-gene association (P=.04). More...	Positive
Shi, J., 2008 (a)		T	OR (95% CI)=1.08 (0.78-1.51) , Z test P-value = 0.63 for Eu...... OR (95% CI)=1.08 (0.78-1.51) , Z test P-value = 0.63 for European samples. More...	No single maker showed evidence of overall association with ...... No single maker showed evidence of overall association with BP. More...	Negative
Maheshwari, M.,2009	T/C		TDT: Raw TDT P-value = 0.26, Adaptive permutation corrected ...... TDT: Raw TDT P-value = 0.26, Adaptive permutation corrected P-value = 0.563 STEPC: sib_tdt P-value = 0.0083, TG P-value = 0.038 More...	No significant allelic association with BP was found, but as...... No significant allelic association with BP was found, but association underlies the previously observed linkage signals in the CNGsample set was found. More...	Positive
Detera-Wadleigh, S. D., 2006	C/T		Fisher P-value = 0.0505 for all, P-value = 0.0832 for BP Onl...... Fisher P-value = 0.0505 for all, P-value = 0.0832 for BP Only More...		Negative

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
DAOA-AS1	DAOA antisense RNA 1	13q33.2	Mapped by Literature SNP
DAOA	D-amino acid oxidase activator	13q33.2	21(13/7/1)

SNPs in LD with rs1341402 (count: 3) View in gBrowse (chr13:105463160..105491996 )

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: 3)

rs_ID	Functional Annotation	r²[population]
rs2226083	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.891[CEU]
rs7989006	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.837[CEU]
rs7995553	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.812[CEU]

Overlap with SZ from cross-disorder studies (count: 3)

Reference	Statistical Result	Description	Result Category
Williams, N. M., 2006	allelic P-value = 0.82 in Schizophrenia	We found no evidence for allelic or genotypic association with any of the polymorphisms studied for schizophrenia. We observed nominally significant evidence (P=.01-.047) for allelic association with 3 of the polymorphisms for bipolar disorder and significant evidence for whole-gene association (P=.04).	Negative
Schumacher, J.,2004	Association analysis:allele P-value = 0.352, OR=1.14, genotype P-value = 0.55, OR=1.48	No significant association was observed in SZ.	Negative
Detera-Wadleigh, S. D., 2006	Fisher P-value = 0.0505 for all, P-value = 0.9667 for SCZ Only		Negative

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