PTSDgene database

Pathway Enrichment Analysis Protein-Protein Interaction Analysis

SNP Report

Basic Info

Name	rs4790904 dbSNP Ensembl
Location	17:66783036 - 66783036(+)
Variant Seq	C
Ancestral Allele	T
Ref Seq	T
Minor Allele Frequence	0.352037
Annotation	upstream_gene_variant; intron_variant
Variant Effect	upstream_gene_variant(ENST00000385208); intron_variant(ENST00000413366)
SIFT Annotation	tolerated
SIFT Variant Effect	tolerated(ENST00000413366)
PolyPhen Annotation	benign
PolyPhen Variant Effect	benign(ENST00000413366)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	n/a
Chromatin State	Weak transcription;Enhancers;Strong transcription;Genic enhancers
No. of Marker's Association Results	9 (Positive: 9; Negative: 0; Trend: 0)
Source	Literature

SNP related association results

Normal genetic study related association results (count: 9)

Reference	Phenotype	Statistical Values	Author Comments	Marker's Category
de Quervain, D. J.,2012	Avoidance symptoms	A allele of rs4790904 with increased avoidance symptoms: P-...... A allele of rs4790904 with increased avoidance symptoms: P-value=0.037. More...	The A allele of rs4790904 was associated with increased avoi...... The A allele of rs4790904 was associated with increased avoidance symptoms. More...	Significant
de Quervain, D. J.,2012	Hyperarousal symptoms	P-value>0.05. P-value>0.05.	SNP rs4790904 was not associated with hyperarousal symptoms. SNP rs4790904 was not associated with hyperarousal symptoms.	Significant
de Quervain, D. J.,2012	PTSD	A allele of rs4790904 with increased risk for PTSD: P-value...... A allele of rs4790904 with increased risk for PTSD: P-value=0.009. More...	The A allele of rs4790904 was associated with increased risk...... The A allele of rs4790904 was associated with increased risk for PTSD. More...	Significant
Liu, Y.,2013	PTSD category B symptom score	Caucasian samples: spearman correlation P-value=0.045; afri...... Caucasian samples: spearman correlation P-value=0.045; african american samples: P-value>0.05 More...	SNP rs4790905 was significantly associated with PTSD B sympt...... SNP rs4790905 was significantly associated with PTSD B symptoms in the Caucasian samples including both current PTSD cases and controls, but not the African-American samples. More...	Significant
Liu, Y.,2013	PTSD category C symptom score	Caucasian samples: spearman correlation P-value=0.016; afri...... Caucasian samples: spearman correlation P-value=0.016; african american samples: P-value>0.05 More...	SNP rs4790906 was significantly associated with PTSD C sympt...... SNP rs4790906 was significantly associated with PTSD C symptoms in the Caucasian samples including both current PTSD cases and controls, but not the African-American samples. More...	Significant
Liu, Y.,2013	PTSD category D symptom score	Caucasian samples: spearman correlation P-value=0.017; afri...... Caucasian samples: spearman correlation P-value=0.017; african american samples: P-value>0.05 More...	SNP rs4790907 was significantly associated with PTSD D sympt...... SNP rs4790907 was significantly associated with PTSD D symptoms in the Caucasian samples including both current PTSD cases and controls, but not the African-American samples. More...	Significant
Liu, Y.,2013	PTSD diagnosis	Caucasian samples: P-value=0.37; african american samples: ...... Caucasian samples: P-value=0.37; african american samples: P-value=0.046 More...	We found a significant association between the categorical g...... We found a significant association between the categorical genotype of SNP rs4790904 with current PTSD diagnosis in the African-Americans, but not the Caucasians. More...	Significant
de Quervain, D. J.,2012	Reexperiencing symptoms	With symptoms of reexperiencing the traumatic event (traumat...... With symptoms of reexperiencing the traumatic event (traumatic memory) in the healthy population: P-value=0.033. More...	PRKCA SNP rs4790904 was significantly associated with sympto...... PRKCA SNP rs4790904 was significantly associated with symptoms of reexperiencing the traumatic event (traumatic memory) with the same direction of effect as with memory for negative information in the healthy population. More...	Significant
Liu, Y.,2013	Total PTSD symptoms	Caucasian samples: spearman correlation P-value=0.02; afric...... Caucasian samples: spearman correlation P-value=0.02; african american samples: P-value>0.05 More...	SNP rs4790904 was significantly associated with total PTSD s...... SNP rs4790904 was significantly associated with total PTSD symptoms in the Caucasian samples including both current PTSD cases and controls, but not the African-American samples. More...	Significant

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

Reference	Phenotype	Environment	Statistical Values	Author Comments	Marker's Category
de Quervain, D. J.,2012	PTSD	Sex	Sex x SNP interaction: P-value >= 0.7. Sex x SNP interaction: P-value >= 0.7.	Sex did not influence the genotype effect on traumatic memor...... Sex did not influence the genotype effect on traumatic memory or PTSD risk. More...	Non-significant

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
MIR634	microRNA 634	17q24.2	Mapped by Literature SNP
PRKCA	protein kinase C, alpha	17q24.2	10(9/0/1)

SNPs in LD with rs4790904 (count: 0)

SNP related eQTL (count: 1)

Gene Symbol	Gene Existed in PTSDgene?	Tissue	Trans/Cis	Source
CRHR1	Yes	Adipose Subcutaneous	cis	GTEx