PTSDgene database

SNP Report

Basic Info
Name rs258747 dbSNP Ensembl
Location 5:143277248 - 143277248(+)
Variant Seq G
Ancestral Allele G
Ref Seq A
Minor Allele Frequence 0.402756
Annotation downstream_gene_variant
Variant Effect downstream_gene_variant(ENST00000231509, ENST00000415690, ENST00000343796, ENST00000394464, ENST00000424646, ENST00000503201, ENST00000504572, ENST00000394466)
SIFT Annotation tolerated
SIFT Variant Effect tolerated(ENST00000378004, ENST00000418236, ENST00000443674, ENST00000274498)
PolyPhen Annotation benign; possibly_damaging
PolyPhen Variant Effect benign(ENST00000378004, ENST00000418236); possibly_damaging(ENST00000443674, ENST00000274498)
rSNP? Yes Link in rVarBase
Related Regulatory Elements n/a
Chromatin State Weak transcription;Strong transcription;Enhancers
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
Lian, Y.,2014 PTSD Logistic regression analysis (after adjusting for age): gen...... Logistic regression analysis (after adjusting for age): genotype (A/A, G/A, G/G): P-value=0.003; allele (A with G): P-value=0.001. More... We demonstrated that the presence of GG and GA genotypes and...... We demonstrated that the presence of GG and GA genotypes and the G allele (rs258747) significantly reduced the risk of PTSD, while presence of the A allele and AA genotype was a positive factor with respect to disease risk. More... Significant

SNP related genes (count: 1)
Approved Symbol Approved Name Location No. of Association Results (Positive/Negative/Trend)
NR3C1 nuclear receptor subfamily 3 group C member 1 5q31-q32 6(2/4/0)

SNPs in LD with rs258747 (count: 9)
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: 9)

SNP related eQTL (count: 1)
Gene Symbol Gene Existed in PTSDgene? Tissue Trans/Cis Source
CRHR1-IT1 Yes Adipose Subcutaneous cis GTEx