PTSDgene database

SNP Report

Basic Info
Name rs1800629 dbSNP Ensembl
Location 6:31575254 - 31575254(+)
Variant Seq A
Ancestral Allele G
Ref Seq G
Minor Allele Frequence 0.0902556
Annotation downstream_gene_variant; upstream_gene_variant
Variant Effect downstream_gene_variant(ENST00000471842, ENST00000489638, ENST00000418386, ENST00000454783); upstream_gene_variant(ENST00000449264)
SIFT Annotation tolerated
SIFT Variant Effect tolerated(ENST00000454783, ENST00000418386)
PolyPhen Annotation benign
PolyPhen Variant Effect benign(ENST00000454783, ENST00000418386)
rSNP? Yes Link in rVarBase
Related Regulatory Elements TF binding region;Chromatin interactive region
Chromatin State Enhancers;Weak transcription;Flanking Active TSS;Bivalent/Poised TSS;Active TSS;Bivalent Enhancer
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
Bruenig, D.,2017(a) CAPS score ANOVA: F(2,280)=3.314, P-value=0.038. Post-hoc comparation: ...... ANOVA: F(2,280)=3.314, P-value=0.038. Post-hoc comparation: AA/AG vs GG: P-value=0.045. More... The GG genotype showing significantly higher CAPS scores tha...... The GG genotype showing significantly higher CAPS scores than the pooled AA/AG genotype. More... Significant

SNP related genes (count: 4)
Approved Symbol Approved Name Location No. of Association Results (Positive/Negative/Trend)
CLIC1 chloride intracellular channel 1 6p21.3 rSNP target
LTA lymphotoxin alpha 6p21.3 Mapped by Literature SNP
SNORA38 small nucleolar RNA, H/ACA box 38 6p21.33 rSNP target
TNF tumor necrosis factor 6p21.3 1(1/0/0)

SNPs in LD with rs1800629 (count: 4)
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: 4)

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