SNP Report

Basic Info

Name	rs1116255 dbSNP Ensembl
Location	13:54914870 - 54914870(+)
Variant Seq	C
Ancestral Allele	C
Ref Seq	T
Minor Allele Frequence	0.219649
Annotation	upstream_gene_variant
SIFT Annotation	deleterious
SIFT Variant Effect	deleterious(ENST00000219022)
PolyPhen Annotation	benign
PolyPhen Variant Effect	benign(ENST00000219022)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	n/a
Chromatin State	Weak transcription
No. of Marker's Association Results	1 (Positive: 0; Negative: 0; Trend: 1)
Source	Literature

SNP related association results

Normal genetic study related association results (count: 1)

Reference	Phenotype	Statistical Values	Author Comments	Marker's Category
Ashley-Koch, A. E.,2015	Current PTSD	In NHW subset: OR=2.19, main effect P-value=5.46E-06. In NHW subset: OR=2.19, main effect P-value=5.46E-06.	This SNP was nominally significant with current PTSD among t...... This SNP was nominally significant with current PTSD among the NHW subset (P-value More...	Trend

G*E study related association result (count: 2)

Reference	Phenotype	Environment	Statistical Values	Author Comments	Marker's Category
Ashley-Koch, A. E.,2015	Current PTSD	Childhood trauma	Logistic regression (additive genetic model) in NHW subset: ...... Logistic regression (additive genetic model) in NHW subset: snp and child trauma interaction P-value=0.37. More...	We haven't observed significant evidence for geneenvironmen...... We haven't observed significant evidence for geneenvironment interactions of this snp with childhood trauma. More...	Non-significant
Ashley-Koch, A. E.,2015	Current PTSD	NTE (number of traumatic events)	Logistic regression (additive genetic model) in NHW subset: ...... Logistic regression (additive genetic model) in NHW subset: snp and total trauma interaction P-value=0.61. More...	We haven't observed significant evidence for geneenvironmen...... We haven't observed significant evidence for geneenvironment interactions of this snp with total trauma. More...	Non-significant

SNP related genes (count: 0)

SNPs in LD with rs1116255 (count: 95)

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

Literature-origin SNPs (count: 0)

LD-proxies (count: 95)

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs9569116	rs1116255	upstream_gene_variant	0.9228[EUR]
rs7318838	rs1116255	intron_variant; non_coding_transcript_variant	0.9357[EUR]; 0.9205[AFR]
rs9597060	rs1116255	upstream_gene_variant	0.9890[EUR]; 0.9793[AFR]; 1.0000[AMR]
rs9563265	rs1116255	intron_variant; non_coding_transcript_variant	0.8059[EUR]
rs9569132	rs1116255	upstream_gene_variant	0.9228[EUR]
rs9569112	rs1116255	upstream_gene_variant	1.0000[EUR]; 0.8757[AMR]
rs1462193	rs1116255	upstream_gene_variant	1.0000[EUR]; 0.8757[AMR]
rs1993777	rs1116255	upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8901[EUR]; 0.8754[AMR]
rs8000818	rs1116255	upstream_gene_variant	0.9675[EUR]; 0.9205[AFR]; 0.8058[AMR]
rs34484169	rs1116255	upstream_gene_variant	0.9675[EUR]
rs2126413	rs1116255	upstream_gene_variant	1.0000[EUR]; 0.8757[AMR]
rs2409580	rs1116255	upstream_gene_variant	0.9675[EUR]
rs1599562	rs1116255	upstream_gene_variant	1.0000[EUR]; 1.0000[AFR]; 1.0000[AMR]
rs11148318	rs1116255	upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8685[AFR]
rs17089847	rs1116255	upstream_gene_variant	0.9228[EUR]
rs9569145	rs1116255	upstream_gene_variant	0.8901[EUR]
rs6561806	rs1116255	upstream_gene_variant	0.9670[EUR]; 0.9691[AFR]; 0.9792[AMR]
rs1580272	rs1116255	upstream_gene_variant	0.9781[EUR]; 1.0000[AFR]; 0.9792[AMR]
rs9569120	rs1116255	upstream_gene_variant	0.9675[EUR]
rs4885494	rs1116255	upstream_gene_variant	0.9571[EUR]; 0.9403[AFR]; 0.8058[AMR]
rs12875707	rs1116255	upstream_gene_variant	0.8042[EUR]
rs9563253	rs1116255	upstream_gene_variant	1.0000[EUR]; 0.8757[AMR]
rs9569129	rs1116255	upstream_gene_variant	1.0000[EUR]; 0.8757[AMR]
rs9569095	rs1116255	upstream_gene_variant	0.8042[EUR]
rs9563256	rs1116255	upstream_gene_variant	1.0000[EUR]; 0.8159[AMR]
rs9563251	rs1116255	upstream_gene_variant	0.9564[EUR]
rs1539235	rs1116255	downstream_gene_variant	0.8042[EUR]
rs9569157	rs1116255	intron_variant; non_coding_transcript_variant	0.8059[EUR]
rs9527299	rs1116255	upstream_gene_variant	0.9571[EUR]; 0.9300[AFR]; 0.8058[AMR]
rs9563267	rs1116255	intron_variant; non_coding_transcript_variant	0.8059[EUR]
rs1841709	rs1116255	upstream_gene_variant	0.9571[EUR]; 0.9403[AFR]
rs2409579	rs1116255	upstream_gene_variant	1.0000[EUR]; 0.8550[AMR]
rs4885518	rs1116255	upstream_gene_variant	0.8395[AFR]
rs35064389	rs1116255	upstream_gene_variant	1.0000[EUR]; 0.8757[AMR]
rs9569134	rs1116255	upstream_gene_variant	1.0000[EUR]; 0.8757[AMR]
rs9569133	rs1116255	upstream_gene_variant	1.0000[EUR]; 0.8757[AMR]
rs2169478	rs1116255	upstream_gene_variant	0.9571[EUR]; 1.0000[AFR]; 1.0000[AMR]
rs1118523	rs1116255	upstream_gene_variant	0.9571[EUR]; 0.9403[AFR]; 0.8058[AMR]
rs71439542	rs1116255	upstream_gene_variant	0.9228[EUR]
rs2409584	rs1116255	upstream_gene_variant	1.0000[EUR]; 1.0000[AFR]; 1.0000[AMR]
rs7320465	rs1116255	upstream_gene_variant	0.8873[EUR]; 0.9292[AFR]; 0.9792[AMR]
rs12584689	rs1116255	upstream_gene_variant	1.0000[EUR]; 0.8757[AMR]
rs9536908	rs1116255	upstream_gene_variant	0.9357[EUR]; 0.9102[AFR]
rs17089845	rs1116255	upstream_gene_variant	0.9675[EUR]
rs9569130	rs1116255	upstream_gene_variant	1.0000[EUR]; 0.8757[AMR]
rs2006684	rs1116255	upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8873[EUR]; 0.8930[AFR]; 0.9211[AMR]
rs9569102	rs1116255	upstream_gene_variant	0.8042[EUR]
rs2050972	rs1116255	upstream_gene_variant	0.8366[EUR]
rs1993776	rs1116255	upstream_gene_variant	0.9357[EUR]; 0.9102[AFR]
rs35242816	rs1116255	upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8481[EUR]
rs9536911	rs1116255	upstream_gene_variant	0.9247[EUR]; 0.9009[AFR]; 0.8058[AMR]
rs6561807	rs1116255	upstream_gene_variant	0.8901[EUR]; 0.8754[AMR]
rs12584803	rs1116255	upstream_gene_variant	0.9890[EUR]; 0.8757[AMR]
rs9569153	rs1116255	intron_variant; non_coding_transcript_variant	0.8363[EUR]
rs9563266	rs1116255	intron_variant; non_coding_transcript_variant	0.8059[EUR]
rs34571320	rs1116255	upstream_gene_variant	1.0000[EUR]; 0.8757[AMR]
rs12856890	rs1116255	intron_variant; non_coding_transcript_variant	0.8059[EUR]
rs9569126	rs1116255	upstream_gene_variant	0.9337[EUR]
rs1599558	rs1116255	upstream_gene_variant	1.0000[EUR]; 0.8757[AMR]
rs9569104	rs1116255	upstream_gene_variant	0.8042[EUR]
rs9563252	rs1116255	upstream_gene_variant	0.9228[EUR]
rs8001846	rs1116255	upstream_gene_variant	1.0000[EUR]; 0.9793[AFR]; 1.0000[AMR]
rs34210014	rs1116255	upstream_gene_variant	0.9675[EUR]
rs9569107	rs1116255	upstream_gene_variant	0.9228[EUR]
rs9569125	rs1116255	upstream_gene_variant	0.9228[EUR]
rs17089846	rs1116255	upstream_gene_variant	1.0000[EUR]; 0.8757[AMR]
rs9569118	rs1116255	upstream_gene_variant	0.9675[EUR]
rs1599561	rs1116255	upstream_gene_variant	0.9675[EUR]; 0.9499[AFR]; 0.8058[AMR]
rs9569117	rs1116255	upstream_gene_variant	0.9675[EUR]
rs12873684	rs1116255	intron_variant; non_coding_transcript_variant	0.8059[EUR]
rs71439545	rs1116255	intron_variant; non_coding_transcript_variant	0.8481[EUR]
rs2409557	rs1116255	intron_variant; non_coding_transcript_variant	0.9890[EUR]; 0.9793[AFR]; 1.0000[AMR]
rs71439537	rs1116255	upstream_gene_variant	0.8042[EUR]
rs9569127	rs1116255	upstream_gene_variant	0.9123[EUR]
rs1979351	rs1116255	upstream_gene_variant	0.8816[AFR]
rs9316747	rs1116255	upstream_gene_variant	1.0000[EUR]; 0.8757[AMR]
rs6561808	rs1116255	intron_variant; non_coding_transcript_variant	0.9357[EUR]; 0.9102[AFR]
rs9563249	rs1116255	upstream_gene_variant	0.9675[EUR]
rs1599557	rs1116255	upstream_gene_variant	0.9675[EUR]
rs9536910	rs1116255	upstream_gene_variant	0.9559[EUR]; 0.9386[AFR]; 1.0000[AMR]
rs9569156	rs1116255	intron_variant; non_coding_transcript_variant	0.8059[EUR]
rs9634858	rs1116255	upstream_gene_variant	1.0000[EUR]; 0.8757[AMR]
rs9563248	rs1116255	upstream_gene_variant	0.9675[EUR]
rs36027061	rs1116255	intron_variant; non_coding_transcript_variant	0.8059[EUR]
rs28644181	rs1116255	upstream_gene_variant	1.0000[EUR]; 0.8757[AMR]
rs4608228	rs1116255	upstream_gene_variant	0.9011[EUR]
rs9563255	rs1116255	upstream_gene_variant	0.9675[EUR]
rs12584885	rs1116255	upstream_gene_variant	1.0000[EUR]; 0.8550[AMR]
rs71199703	rs1116255	upstream_gene_variant	0.9123[EUR]
rs4547236	rs1116255	upstream_gene_variant	0.9778[EUR]; 0.8757[AMR]
rs9569128	rs1116255	upstream_gene_variant	0.9778[EUR]; 0.8757[AMR]
rs9569152	rs1116255	intron_variant; non_coding_transcript_variant	0.8059[EUR]
rs71439546	rs1116255	intron_variant; non_coding_transcript_variant	0.8059[EUR]
rs7326733	rs1116255	upstream_gene_variant	0.9559[EUR]; 0.9386[AFR]; 1.0000[AMR]
rs9569103	rs1116255	upstream_gene_variant	0.8042[EUR]

SNP related eQTL (count: 1)

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