SNP Report

Basic Info

Name	rs717947 dbSNP Ensembl
Location	4:33652135 - 33652135(+)
Variant Seq	T
Ancestral Allele	C
Ref Seq	C
Minor Allele Frequence	0.205671
Annotation	upstream_gene_variant
SIFT Annotation	deleterious; tolerated
SIFT Variant Effect	deleterious(ENST00000621961); tolerated(ENST00000511884)
PolyPhen Annotation	benign
PolyPhen Variant Effect	benign(ENST00000511884, ENST00000621961)
rSNP?	No Link in rVarBase
Related Regulatory Elements	n/a
Chromatin State	Inactive region
No. of Marker's Association Results	1 (Positive: 1; Negative: 0; 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
Almli, L. M.,2015	PTSD Symptoms as measured by the quantitave CAPS scores	In (SBPBC cohort) discovery stage: (sex and top three princ...... In (SBPBC cohort) discovery stage: (sex and top three principal components as covariates) N=147, B (SE)=31.34 (5.19), P-value=1.28E-08; categorical PTSD diagnosis measure: OR=8.6, 95%CI=3.5-21.6, P-value=3.84E-06; self-reported PTSD symptoms: N=147, B (SE)=17.37 (3.10), P-value=1.203E-07. The main effect of rs717947 for CAPS scores after controlling for early childhood trauma exposure or overall negative life events: [Covariate: Early Trauma Inventory, N=146, B (SE)=31.5 (5.2), P-value=1.13E-08; Negative life events, N=146, B (SE)=24.9 (4.3), P-value=3.29E-08]. In (GTP cohort) replication stage: in female, N=2006, OR=1.25, CI=1.1-1.5, P-value=0.005; in male, N=862, P-value=0.37 More...	The GWAS yielded one genome-wide significant SNP, rs717947 w...... The GWAS yielded one genome-wide significant SNP, rs717947 with current CAPS score. Sensitivity analysis covarying for self-reported race instead of the top three principal components showed similar results for the association between rs717947 and PTSD symptoms (data not shown). Follow-up analysis of SNP rs717947 showed that this SNP is robust to different measures of PTSD, both categorical and self-reported measures. In both cases, the main effect of rs717947 remained genome-wide significant for CAPS scores after controlling for early childhood trauma exposure or overall negative life events. In (GTP cohort) replication stage: in females, we found that carriers of the risk allele (T) had increased odds of PTSD diagnosis; in contrast, no association was found in males. More...	Significant

SNP related genes (count: 0)

SNPs in LD with rs717947 (count: 48)

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: 1)

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

rs7684329		1(0/0/1)	0.8083[EUR]

LD-proxies (count: 47)

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs28634392	rs717947	upstream_gene_variant	0.8048[EUR]
rs1454608	rs717947	upstream_gene_variant	0.8835[EUR]
rs16989140	rs7684329 rs717947	upstream_gene_variant	1.0000[EUR]; 0.9891[AFR]; 0.9806[AMR]
rs7685939	rs717947	upstream_gene_variant	0.8138[EUR]
rs6832462	rs13104973 rs7684329 rs717947	intron_variant; non_coding_transcript_variant	0.8083[EUR]
rs10517294	rs13104973 rs7684329 rs717947	intron_variant; non_coding_transcript_variant	0.8083[EUR]
rs2124029	rs717947	upstream_gene_variant	0.8138[EUR]
rs10023739	rs717947	upstream_gene_variant	0.8138[EUR]
rs73132844	rs13104973 rs7684329 rs717947	intron_variant; non_coding_transcript_variant	0.8083[EUR]
rs13141649	rs717947	upstream_gene_variant	0.8834[EUR]; 0.9138[AFR]; 0.9803[AMR]
rs13134089	rs13104973 rs7684329 rs717947	upstream_gene_variant	0.8083[EUR]
rs61139508	rs13104973 rs7684329 rs717947	upstream_gene_variant	0.8329[EUR]
rs7680059	rs13104973 rs7684329 rs717947	upstream_gene_variant	0.8706[EUR]
rs12645598	rs13104973 rs7684329 rs717947	upstream_gene_variant	0.8083[EUR]
rs34151233	rs13104973 rs7684329 rs717947	upstream_gene_variant	0.8325[EUR]
rs35440893	rs717947	upstream_gene_variant	0.8835[EUR]; 0.8817[AFR]; 0.9803[AMR]
rs1378041	rs717947	upstream_gene_variant	0.8835[EUR]; 0.8721[AFR]; 0.9240[AMR]
rs67441316	rs13104973 rs7684329 rs717947	upstream_gene_variant	0.8329[EUR]
rs16989190	rs13104973 rs7684329 rs717947	upstream_gene_variant	0.8452[EUR]
rs67239648	rs13104973 rs7684329 rs717947	upstream_gene_variant	0.8452[EUR]
rs66770627	rs13104973 rs7684329 rs717947	intron_variant; non_coding_transcript_variant	0.8083[EUR]
rs59660596	rs13104973 rs7684329 rs717947	upstream_gene_variant	0.8329[EUR]
rs35639548	rs13104973 rs7684329 rs717947	upstream_gene_variant	0.8329[EUR]
rs6852504	rs13104973 rs7684329 rs717947	upstream_gene_variant	0.8706[EUR]
rs67906834	rs13104973 rs7684329 rs717947	upstream_gene_variant	0.8452[EUR]
rs28549134	rs717947	upstream_gene_variant	0.8138[EUR]
rs12641122	rs717947	upstream_gene_variant	0.8963[EUR]; 0.8935[AFR]; 0.9803[AMR]
rs35045625	rs717947	upstream_gene_variant	0.8270[AMR]
rs13135144	rs717947	upstream_gene_variant	0.8138[EUR]
rs1454607	rs717947	upstream_gene_variant	0.8835[EUR]
rs12649294	rs717947	upstream_gene_variant	0.8138[EUR]
rs12648086	rs13104973 rs7684329 rs717947	upstream_gene_variant	0.8963[EUR]; 0.9043[AFR]; 0.9422[AMR]
rs7688152	rs13104973 rs7684329 rs717947	upstream_gene_variant	0.8083[EUR]
rs34951063	rs13104973 rs7684329 rs717947	upstream_gene_variant	0.8835[EUR]; 0.8610[AFR]; 0.9045[AMR]
rs7672940	rs13104973 rs7684329 rs717947	upstream_gene_variant	0.8083[EUR]
rs67281747	rs13104973 rs7684329 rs717947	upstream_gene_variant	0.8452[EUR]
rs13147878	rs13104973 rs7684329 rs717947	upstream_gene_variant	0.8452[EUR]
rs7675932	rs717947	upstream_gene_variant	0.8138[EUR]
rs6811233	rs717947	upstream_gene_variant	0.8048[EUR]
rs1454600	rs7684329 rs717947	upstream_gene_variant	1.0000[EUR]; 0.9891[AFR]; 0.9806[AMR]
rs1822681	rs13104973 rs7684329 rs717947	intron_variant; non_coding_transcript_variant	0.8083[EUR]
rs73125178	rs717947	upstream_gene_variant	0.8138[EUR]
rs16989137	rs717947	upstream_gene_variant	0.8138[EUR]
rs6830471	rs717947	upstream_gene_variant	0.8138[EUR]
rs9998025	rs717947	upstream_gene_variant	0.8048[EUR]
rs35107776	rs13104973 rs7684329 rs717947	upstream_gene_variant	0.8329[EUR]
rs61548475	rs13104973 rs7684329 rs717947	upstream_gene_variant	0.8834[EUR]; 0.9246[AFR]; 0.9240[AMR]

SNP related eQTL (count: 1)

Gene Symbol	Gene Existed in PTSDgene?	Tissue	Trans/Cis	Source
CRHR1-IT1	Yes	Adipose Subcutaneous	cis	GTEx