SNP Report

Basic Info

Name	rs4908699 dbSNP Ensembl
Location	chr1:7845214 - 7845214(1)
Variant Alleles	G/A
Ancestral Allele	G
Minor Allele	A
Minor Allele Frequence	0.0926518
Functional Annotation	downstream_gene_variant; intron_variant.
Consequence to Transcript	downstream_gene_variant(ENST00000054668, ENST00000361696, ENST00000361923, ENST00000377532, ENST00000494684, ENST00000613533, ENST00000614998); intron_variant(ENST00000377516)
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
Mansour, H. A., 2006	A/G		TDT P-value = 0.398 in the samples combined, Pittsburgh Tren...... TDT P-value = 0.398 in the samples combined, Pittsburgh Trends test=0.47 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)
UTS2	urotensin 2	1p36	Mapped by Literature SNP

SNPs in LD with rs4908699 (count: 11) View in gBrowse (chr1:7724378..7859303 )

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]
rs12061787	intron_variant; upstream_gene_variant	0.937[CEU]
rs12741937	intron_variant; non_coding_transcript_variant	1.0[CEU]
rs697674	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0[CEU]
rs1012477	intron_variant; upstream_gene_variant	1.0[CEU]; 1.0[TSI]
rs4908694	downstream_gene_variant; intron_variant	1.0[CEU]; 1.0[TSI]
rs697675	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0[CEU]; 1.0[TSI]
rs4908688	intron_variant; upstream_gene_variant	0.941[CEU]
rs707457	downstream_gene_variant; upstream_gene_variant	1.0[CEU]; 1.0[TSI]
rs6693805	intron_variant	0.878[CEU]
rs17374292	intron_variant; non_coding_transcript_variant	1.0[CEU]
rs17374781		0.938[CEU]

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

Reference	Statistical Result	Description	Result Category
Mansour, H. A., 2006	TDT P-value = 0.352, Trends test=0.161 for Pittsburgh SZ/SZA		Negative

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