SNP Report

Basic Info

Name	rs588765 dbSNP Ensembl
Location	15:78573083 - 78573083(+)
Variant Seq	C
Ancestral Allele	C
Ref Seq	T
Minor Allele Frequence	0.275559
Annotation	intron_variant
Variant Effect	intron_variant(ENST00000299565, ENST00000559554)
SIFT Annotation	tolerated
SIFT Variant Effect	tolerated(ENST00000044462, ENST00000413382, ENST00000559154, ENST00000559948, ENST00000559365, ENST00000560217, ENST00000559082, ENST00000560737, ENST00000558094, ENST00000558281, ENST00000559437, ENST00000559146)
PolyPhen Annotation	benign
PolyPhen Variant Effect	benign(ENST00000044462, ENST00000413382, ENST00000559154, ENST00000559948, ENST00000559365, ENST00000560217, ENST00000559082, ENST00000560737, ENST00000558094, ENST00000558281, ENST00000559437, ENST00000559146)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	Chromatin interactive region
Chromatin State	ZNF genes & repeats;Weak transcription
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
Kimbrel, N. A.,2015	PTSD	In the NHW sample, main effect: P-value=0.02006. In the NHW sample, main effect: P-value=0.02006.	Nominally significant associations (p<.05) were observed, bu...... Nominally significant associations (p<.05) were observed, but it didn't met multiple-testing threshold. More...	Significant

G*E study related association result (count: 1)

Reference	Phenotype	Environment	Statistical Values	Author Comments	Marker's Category
Kimbrel, N. A.,2015	PTSD	Smoking status	GxE interactions among NHW participants: P-value=0.04947. GxE interactions among NHW participants: P-value=0.04947.	Nominally significant associations (p<.05) were observed, bu...... Nominally significant associations (p<.05) were observed, but it didn't met multiple-testing threshold. More...	Significant

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
CHRNA5	cholinergic receptor, nicotinic alpha 5	15q24	2(1/1/0)

SNPs in LD with rs588765 (count: 21)

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: 21)

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs680244	rs588765	upstream_gene_variant; intron_variant	0.9674[EUR]; 0.9006[AMR]
rs11637635	rs588765	downstream_gene_variant; intron_variant	0.8454[AFR]; 0.8222[AMR]
rs601079	rs588765	upstream_gene_variant; intron_variant	0.9728[EUR]; 0.9006[AMR]
rs12911602	rs588765	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant	0.9353[EUR]; 0.9108[AMR]
rs6495306	rs588765	intron_variant	1.0000[EUR]; 0.9894[AFR]; 1.0000[AMR]
rs1878399	rs588765	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9043[EUR]; 0.8297[AMR]
rs621849	rs588765	upstream_gene_variant; intron_variant	0.9728[EUR]; 0.9006[AMR]
rs6495307	rs588765	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant	0.9301[EUR]; 0.9108[AMR]
rs3743077	rs588765	upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9353[EUR]; 0.8949[AMR]
rs514743	rs588765	downstream_gene_variant; upstream_gene_variant; intron_variant	0.8074[AMR]
rs57945453	rs588765	intron_variant	0.8032[EUR]; 0.8232[AMR]
rs472054	rs588765	downstream_gene_variant; upstream_gene_variant; 3_prime_UTR_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8343[AFR]; 0.8074[AMR]
rs692780	rs588765	downstream_gene_variant; intron_variant	0.8222[AMR]
rs660652	rs588765	downstream_gene_variant; upstream_gene_variant; 3_prime_UTR_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8343[AFR]; 0.8074[AMR]
rs647041	rs588765	downstream_gene_variant; upstream_gene_variant; intron_variant	0.9459[EUR]; 0.9160[AFR]; 0.9546[AMR]
rs2456019	rs588765	upstream_gene_variant; intron_variant	0.8074[AMR]
rs8025188	rs588765	downstream_gene_variant; non_coding_transcript_exon_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8732[EUR]
rs555018	rs588765	downstream_gene_variant; upstream_gene_variant; intron_variant	0.9566[EUR]; 0.9789[AFR]; 0.9695[AMR]
rs12901300	rs588765	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant	0.9353[EUR]; 0.9108[AMR]
rs61012457	rs588765	intron_variant	0.8032[EUR]; 0.8232[AMR]
rs481134	rs588765	downstream_gene_variant; intron_variant	0.9566[EUR]; 0.9787[AFR]; 0.9695[AMR]

SNP related eQTL (count: 1)

Gene Symbol	Gene Existed in PTSDgene?	Tissue	Trans/Cis	Source
RP11-259G18.3	No	Adipose Subcutaneous	cis	GTEx