PTSDgene database

SNP Report

Basic Info
Name rs406001 dbSNP Ensembl
Location 7:51938719 - 51938719(+)
Variant Seq C
Ancestral Allele T
Ref Seq T
Minor Allele Frequence 0.0712859
Annotation downstream_gene_variant
SIFT Annotation deleterious_-_low_confidence; tolerated
SIFT Variant Effect deleterious_-_low_confidence(ENST00000395540); tolerated(ENST00000632460, ENST00000265136, ENST00000441453, ENST00000395542)
PolyPhen Annotation benign; possibly_damaging
PolyPhen Variant Effect benign(ENST00000441453); possibly_damaging(ENST00000632460, ENST00000395540, ENST00000265136, ENST00000395542)
rSNP? No Link in rVarBase
Related Regulatory Elements n/a
Chromatin State Inactive region
No. of Marker's Association Results 2 (Positive: 1; Negative: 1; Trend: 0)
Source Literature

SNP related association results
Normal genetic study related association results (count: 2)
Reference Phenotype Statistical Values Author Comments Marker's Category
Xie, P.,2013 Lifetime PTSD Whole Cohort of European Americans: in GWAS,P-value=3.97E-0...... Whole Cohort of European Americans: in GWAS,P-value=3.97E-08,in replication,P-value=0.95,in combined, P-value=2.77E-04;Trauma Exposed European Americans: in GWAS,P-value=1.14E-07,in replication,P-value=0.41,in combined, P-value=3.41E-03. More... In EAs,they observed that one SNP on chromosome 7p12, rs4060...... In EAs,they observed that one SNP on chromosome 7p12, rs406001, exceeded genome-wide significance. More... Significant
Almli, L. M.,2014 PTSD symptoms (mPSS) Linear regression, main effect P-value=0.34 Linear regression, main effect P-value=0.34 They did not replicate as main effects in associations with ...... They did not replicate as main effects in associations with PTSD symptoms in this study. More... Non-significant
G*E study related association result (count: 1)
Reference Phenotype Environment Statistical Values Author Comments Marker's Category
Almli, L. M.,2014 PTSD symptoms (mPSS) Childhood trauma Linear regression, GxE P-value(standard regression model)=0....... Linear regression, GxE P-value(standard regression model)=0.0006, GxE P-value(adjusted with robust standard errors with R package geepack)=0.002. More... We found a significant genotype and environment interaction ...... We found a significant genotype and environment interaction (G x E) with childhood trauma in our AA population. More... Significant


SNP related genes (count: 1)
Approved Symbol Approved Name Location No. of Association Results (Positive/Negative/Trend)
COBL cordon-bleu WH2 repeat protein 7p12.2-p12.1 2(1/1/0)

SNPs in LD with rs406001 (count: 35)
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)

LD-proxies (count: 34)


SNP related eQTL (count: 1)
Gene Symbol Gene Existed in PTSDgene? Tissue Trans/Cis Source
LRRC37A4P No Adipose Subcutaneous cis GTEx