PTSDgene database

SNP Report

Basic Info
Name rs12898919 dbSNP Ensembl
Location 15:78588235 - 78588235(+)
Variant Seq C
Ancestral Allele G
Ref Seq G
Minor Allele Frequence 0.0147764
Annotation downstream_gene_variant; upstream_gene_variant; intron_variant
Variant Effect downstream_gene_variant(ENST00000559002, ENST00000567141, ENST00000559658, ENST00000348639); upstream_gene_variant(ENST00000559576); intron_variant(ENST00000394802, ENST00000299565, ENST00000559554)
SIFT Annotation deleterious
SIFT Variant Effect deleterious(ENST00000299565)
PolyPhen Annotation probably_damaging
PolyPhen Variant Effect probably_damaging(ENST00000299565)
rSNP? Yes Link in rVarBase
Related Regulatory Elements Chromatin interactive region
Chromatin State 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, 95% confidence interval (CI)=1.44-3.83, P...... In the NHW sample, 95% confidence interval (CI)=1.44-3.83, P-value=0.0006114, an ad hoc allele test(C allele vs. G allele): 95%CI= 1.380-3.578, P-value=0.0010. More... A different SNP (rs12898919) in the CHRNA5 gene provided evi...... A different SNP (rs12898919) in the CHRNA5 gene provided evidence for a main effect on PTSD risk in the NHW sample, and this association met correction for multiple testing. Specifically, we found that rs12898919 of the CHRNA5 gene was significantly associated with having a current PTSD diagnosis, such that for each additional C allele, the odds of PTSD increased by 2.35. An ad hoc allele test was conducted to ensure the genotype of the one participant that was homozygous for the C allele was not driving the observed association with this SNP. The association remained significant in the allele test (C allele vs. G allele), such that those with the C allele were 2.22 times as likely as those with the G allele to have PTSD. 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=0.4988. GxE interactions among NHW participants: P-value=0.4988. No GxE interactions were statistically significant among NHW...... No GxE interactions were statistically significant among NHW participants. More... Non-significant


SNP related genes (count: 2)
Approved Symbol Approved Name Location No. of Association Results (Positive/Negative/Trend)
CHRNA3 cholinergic receptor, nicotinic alpha 3 15q24 1(0/1/0)
CHRNA5 cholinergic receptor, nicotinic alpha 5 15q24 2(1/1/0)

SNPs in LD with rs12898919 (count: 18)
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: 18)


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