SNP Report

Basic Info

Name	rs9462341 dbSNP Ensembl
Location	chr6:37643605 - 37643605(1)
Variant Alleles	A/T
Ancestral Allele	T
Minor Allele	A
Minor Allele Frequence	0.472444
Functional Annotation	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant.
Consequence to Transcript	downstream_gene_variant(ENST00000510077); intron_variant(ENST00000418178, ENST00000434837, ENST00000502298, ENST00000505425); NMD_transcript_variant(ENST00000502298); upstream_gene_variant(ENST00000373401, ENST00000503419)
No. of Studies	1 (Positive: 0; Negative: 1; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	YES

SNP related studies (count: 1)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Li, J.,2011(a)	A/T		Single SNP analyses: allele, P-value = 0.2834, OR[95%CI]=1.0...... Single SNP analyses: allele, P-value = 0.2834, OR[95%CI]=1.0674[0.9475, 1.2026], genotype, P-value = 0.1713 for BP More...	No significant association was observed. No significant association was observed.	Negative

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
MDGA1	MAM domain containing glycosylphosphatidylinositol anchor 1	6p21	1(1/0/0)

SNPs in LD with rs9462341 (count: 3) View in gBrowse (chr6:37641529..37643605 )

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]
rs3905219	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[JPT]
rs4714089	downstream_gene_variant; intron_variant; upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs9462340	downstream_gene_variant; intron_variant; upstream_gene_variant	1.0[CHB]; 1.0[JPT]

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

Reference	Statistical Result	Description	Result Category
Li, J.,2011(a)	Single SNP analyses:allele, P-value = 0.0267(0.3417), OR[95%CI]=0.8684[0.7665, 0.9838], genotype, P-value = 0.0196(0.2666 after permutations) for SZ	No significant association was observed.	Negative

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

Reference	Statistical Result	Description	Result Category
Li, J.,2011(a)	Single SNP analyses:allele, P-value = 0.0303(0.0902), OR[95%CI]=0.8748[0.7751, 0.9874], genotype, P-value = 0.082 for MDD	No significant association was observed.	Negative