SNP Report

Basic Info

Name	rs7604404 dbSNP Ensembl
Location	2:172443590 - 172443590(+)
Variant Seq	A
Ancestral Allele	A
Ref Seq	C
Minor Allele Frequence	0.359824
Annotation	intron_variant
Variant Effect	intron_variant(ENST00000442250, ENST00000458358, ENST00000409080, ENST00000409532, ENST00000412899, ENST00000264107)
SIFT Annotation	tolerated
SIFT Variant Effect	tolerated(ENST00000409080, ENST00000264107, ENST00000458358, ENST00000442250)
PolyPhen Annotation	benign
PolyPhen Variant Effect	benign(ENST00000409080, ENST00000264107, ENST00000458358, ENST00000442250)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	Chromatin interactive region;lncRNA
Chromatin State	Enhancers;Weak transcription;Genic enhancers
No. of Marker's Association Results	1 (Positive: 0; Negative: 1; Trend: 0)
Source	Literature

SNP related association results

Normal genetic study related association results (count: 1)

Reference	Phenotype	Statistical Values	Author Comments	Marker's Category
Nelson, E. C.,2014	PTSD	P-value=0.0063, OR=0.76 P-value=0.0063, OR=0.76	Although the association of this SNP is of considerably lowe...... Although the association of this SNP is of considerably lower magnitude, it is interesting to note. More...	Non-significant

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
ITGA6	integrin subunit alpha 6	2q31.1	1(0/1/0)

SNPs in LD with rs7604404 (count: 7)

The LD data used here is based on 1000 Genome Phase I. LD SNP pairs were selected with a threshold r²<=0.8.

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs12616959	rs7604404	upstream_gene_variant; intron_variant	0.8122[EUR]
rs3792254	rs7604404	upstream_gene_variant; intron_variant	0.8122[EUR]
rs9287954	rs7604404	intron_variant	0.9883[EUR]
rs7584977	rs7604404	upstream_gene_variant; intron_variant	0.8122[EUR]
rs7596259	rs7604404	intron_variant	0.9768[EUR]
rs7584971	rs7604404	upstream_gene_variant; intron_variant	0.8122[EUR]
rs58514604	rs7604404	intron_variant	1.0000[EUR]

SNP related eQTL (count: 1)

Gene Symbol	Gene Existed in PTSDgene?	Tissue	Trans/Cis	Source
RP11-707O23.5	No	Adipose Subcutaneous	cis	GTEx