PTSDgene database

SNP Report

Basic Info
Name rs1316971 dbSNP Ensembl
Location 15:78638168 - 78638168(+)
Variant Seq G,T
Ancestral Allele A
Ref Seq A
Minor Allele Frequence 0.442492
Annotation intron_variant; NMD_transcript_variant; non_coding_transcript_variant
Variant Effect intron_variant(ENST00000559849, ENST00000412074, ENST00000560511, ENST00000261751); NMD_transcript_variant(ENST00000559849); non_coding_transcript_variant(ENST00000560511)
SIFT Annotation deleterious_-_low_confidence; deleterious
SIFT Variant Effect deleterious_-_low_confidence(ENST00000559849); deleterious(ENST00000412074, ENST00000261751)
PolyPhen Annotation unknown; possibly_damaging; probably_damaging
PolyPhen Variant Effect unknown(ENST00000559849); possibly_damaging(ENST00000261751); probably_damaging(ENST00000412074)
rSNP? No Link in rVarBase
Related Regulatory Elements n/a
Chromatin State Inactive region
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, main effect: P-value=0.003377. In the NHW sample, main effect: P-value=0.003377. Nominally significant associations (p<.05) were observed, bu...... Nominally significant associations (p<.05) were observed, but it didn't met multiple-testing threshold. 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=0.6343. GxE interactions among NHW participants: P-value=0.6343. 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)
CHRNA4 cholinergic receptor, nicotinic alpha 4 20q13.33 1(1/0/0)
CHRNB4 cholinergic receptor, nicotinic beta 4 15q24 Mapped by Literature SNP, Mapped by LD-proxy, rSNP target

SNPs in LD with rs1316971 (count: 5)
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: 5)


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