SNP Report

Basic Info

Name	rs1409497 dbSNP Ensembl
Location	chr13:23343142 - 23343142(1)
Variant Alleles	A/G
Ancestral Allele	A
Minor Allele	G
Minor Allele Frequence	0.0449281
Functional Annotation	intron_variant.
Consequence to Transcript	intron_variant(ENST00000382292, ENST00000402364, ENST00000423156, ENST00000455470)
No. of Studies	1 (Positive: 0; Negative: 1; 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
Bergen, S. E.,2012		A	logistic regression: P-value > E-05 logistic regression: P-value > E-05	No significant association was observed in BD. No significant association was observed in BD.	Negative

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
SACS	sacsin molecular chaperone	13q11	1(0/1/0)
SGCG	sarcoglycan, gamma (35kDa dystrophin-associated glycoprotein)	13q12-q13	2(0/2/0)

SNPs in LD with rs1409497 (count: 8) View in gBrowse (chr13:23294092..23357994 )

The LD data used here is based on HapMap rel#27. LD SNP pairs were selected with a threshold r²<=0.8.

rs_ID	Functional Annotation	r²[population]
rs10507329	intron_variant; upstream_gene_variant	0.913[CEU]; 0.95[TSI]
rs4770431	intron_variant	0.913[CEU]; 1.0[TSI]
rs1536365	5_prime_UTR_variant; synonymous_variant; upstream_gene_variant	0.918[CEU]; 0.952[TSI]
rs2031640	5_prime_UTR_variant; missense_variant; upstream_gene_variant	0.831[CEU]; 0.952[TSI]
rs4769255	intron_variant	1.0[TSI]
rs4569110	intron_variant	0.952[TSI]
rs4770434	intron_variant	1.0[CEU]
rs2031641	intron_variant; upstream_gene_variant	0.831[CEU]; 0.95[TSI]

Overlap with SZ from cross-disorder studies (count: 1)

Reference	Statistical Result	Description	Result Category
Bergen, S. E.,2012	logistic regression:for SZ full sample, OR=1.39, P-value = 5.17E-06	No significant association was observed in SZ.	Negative

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