SNP Report

Basic Info

Name	rs228729 dbSNP Ensembl
Location	chr1:7785635 - 7785635(1)
Variant Alleles	T/C
Ancestral Allele	C
Minor Allele	T
Minor Allele Frequence	0.275559
Functional Annotation	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant.
Consequence to Transcript	downstream_gene_variant(ENST00000054666); intron_variant(ENST00000361923, ENST00000377532, ENST00000377541, ENST00000473653, ENST00000613533, ENST00000614998); non_coding_transcript_variant(ENST00000473653); upstream_gene_variant(ENST00000602883)
No. of Studies	3 (Positive: 0; Negative: 3; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 3)

Reference	Allele Change	Statistical Values	Author Comments	Result Category
Abou Jamra, R, 2008 (b)	A/G	Initial sample: Armitage P-value = 0.929; Initial sample: Armitage P-value = 0.929;	none of the four analyzed SNP markers revealed significant a...... none of the four analyzed SNP markers revealed significant association to bipolar affective disorder More...	Negative
Yosifova, A.,2009	T/C	Allelic association: P-value = 0.14 Allelic association: P-value = 0.14	No significant association was observed No significant association was observed	Negative
Mansour, H. A., 2006	C/T	TDT P-value = 0.836 in the samples combined, Pittsburgh Tren...... TDT P-value = 0.836 in the samples combined, Pittsburgh Trends test=0.08 for BDI More...	The loci tested did not show significant differences between...... The loci tested did not show significant differences between sites in the transmission rate. More...	Negative

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
PER3	period circadian clock 3	1p36.23	7(3/4/0)
VAMP3	vesicle-associated membrane protein 3	1p36.23	1(0/1/0)

SNPs in LD with rs228729 (count: 2) View in gBrowse (chr1:7785635..7830896 )

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]
rs228665		intron_variant; upstream_gene_variant	0.958[CEU]
rs10864315		downstream_gene_variant; intron_variant	0.842[CEU]; 0.82[TSI]

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

Reference	Statistical Result	Description	Result Category
Mansour, H. A., 2006	TDT P-value = 0.914, Trends test=0.028 for Pittsburgh SZ/SZA		Negative

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