SNP Report

Basic Info

Name	rs909685 dbSNP Ensembl
Location	chr22:39351666 - 39351666(1)
Variant Alleles	T/A
Ancestral Allele	A
Minor Allele	T
Minor Allele Frequence	0.49381
Functional Annotation	intron_variant; NMD_transcript_variant; non_coding_transcript_variant.
Consequence to Transcript	intron_variant(ENST00000216155, ENST00000318801, ENST00000328933, ENST00000406293, ENST00000415332, ENST00000489206); NMD_transcript_variant(ENST00000415332); non_coding_transcript_variant(ENST00000489206)
No. of Studies	2 (Positive: 1; Negative: 1; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 2)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Yosifova, A.,2009	A/T		Allelic association: 1st screening: P-value = 0.1, 2nd scree...... Allelic association: 1st screening: P-value = 0.1, 2nd screening: P-value = 0.16, total: P-value = 0.9 More...	No significant association was observed No significant association was observed	Negative
Verma, R.,2005(a)	T/A		Fisher's exact test: allele P-value = 0.028, chi-square test...... Fisher's exact test: allele P-value = 0.028, chi-square test: genotype P-value = 0.1 in BPAD More...	Significant association was observed in allelic association. Significant association was observed in allelic association.	Positive

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
SYNGR1	synaptogyrin 1	22q13	3(2/1/0)

SNPs in LD with rs909685 (count: 2) View in gBrowse (chr22:39351666..39362248 )

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

rs_ID	Literature-origin SNPs with LD	Functional Annotation	r²[population]
rs2069235		intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CEU]; 0.874[CHB]; 1.0[JPT]
rs715503		intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.826[CHB]

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

Reference	Statistical Result	Description	Result Category
Verma, R.,2005(a)	Fisher's exact test:allele P-value = 0.007, chi-square test:genotype P-value = 0.025 in SCZ	Significant association was observed in allelic association.	Positive

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