SNP Report

Basic Info

Name	rs4460839 dbSNP Ensembl
Location	11:113451074 - 113451074(+)
Variant Seq	T
Ancestral Allele	T
Ref Seq	C
Minor Allele Frequence	0.247404
Annotation	upstream_gene_variant; intron_variant; non_coding_transcript_variant
Variant Effect	upstream_gene_variant(ENST00000577203, ENST00000543292); intron_variant(ENST00000540600, ENST00000346454, ENST00000542616, ENST00000362072); non_coding_transcript_variant(ENST00000540600)
SIFT Annotation	tolerated
SIFT Variant Effect	tolerated(ENST00000362072, ENST00000543292, ENST00000538967, ENST00000544518, ENST00000542968, ENST00000346454)
PolyPhen Annotation	benign
PolyPhen Variant Effect	benign(ENST00000362072, ENST00000543292, ENST00000538967, ENST00000544518, ENST00000542968, ENST00000346454)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	n/a
Chromatin State	Weak transcription
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
Duan, Z.,2015	PTSD diagnosis	Allele dose analysis model: P-value=0.17; Dominant effect: ...... Allele dose analysis model: P-value=0.17; Dominant effect: P-value=0.37; Recessive effect: P-value=0.08. More...	No significant results. No significant results.	Non-significant

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
MIR4301	microRNA 4301	11	Mapped by Literature SNP, Mapped by LD-proxy
DRD2	dopamine receptor D2	11q23.2	18(11/7/0)

SNPs in LD with rs4460839 (count: 12)

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	Annotation	No. of Association Results(Positive/Negative/Trend)	r²[population]

rs4274224	downstream_gene_variant(ENST00000577203); upstream_gene_variant(ENST00000543292); intron_variant(ENST00000346454, ENST00000362072, ENST00000542616, ENST00000540600); non_coding_transcript_variant(ENST00000540600)	1(0/1/0)	0.8548[ASN]

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs10891553	rs4460839	intron_variant; non_coding_transcript_variant	0.8096[ASN]
rs11214613	rs4460839	intron_variant; non_coding_transcript_variant	0.8096[ASN]
rs4581480	rs4460839	upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.9675[ASN]
rs4245147	rs4274224 rs4460839	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8548[ASN]
rs4245146	rs4274224 rs4460839	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8548[ASN]
rs11214612	rs4460839	intron_variant; non_coding_transcript_variant	0.8096[ASN]
rs4936274	rs4460839	intron_variant; non_coding_transcript_variant	0.8096[ASN]
rs4936271	rs4274224 rs4460839	downstream_gene_variant; upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8548[ASN]
rs4936270	rs4460839	downstream_gene_variant; 5_prime_UTR_variant; intron_variant; non_coding_transcript_variant	1.0000[ASN]
rs4245148	rs4460839	downstream_gene_variant; upstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0000[ASN]
rs4936272	rs4274224 rs4460839	downstream_gene_variant; upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8548[ASN]

SNP related eQTL (count: 1)

Gene Symbol	Gene Existed in PTSDgene?	Tissue	Trans/Cis	Source
TMPRSS5	No	Adipose Subcutaneous	cis	GTEx