PTSDgene database

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)


SNP related eQTL (count: 1)
Gene Symbol Gene Existed in PTSDgene? Tissue Trans/Cis Source
RP11-259G18.3 No Adipose Subcutaneous cis GTEx