PTSDgene database

Pathway Enrichment Analysis Protein-Protein Interaction Analysis

SNP Report

Basic Info

Name	rs148139959 dbSNP Ensembl
Location	4:46370908 - 46370908(+)
Variant Seq	A
Ancestral Allele	C
Ref Seq	C
Minor Allele Frequence	0.00279553
Annotation	intron_variant; NMD_transcript_variant
Variant Effect	intron_variant(ENST00000507069, ENST00000381620, ENST00000540012, ENST00000507460, ENST00000514090, ENST00000514193, ENST00000503806, ENST00000630416, ENST00000515082, ENST00000510861, ENST00000510233, ENST00000506961, ENST00000356504, ENST00000513005); NMD_transcript_variant(ENST00000514193, ENST00000630416, ENST00000510233, ENST00000513005)
SIFT Annotation	deleterious
SIFT Variant Effect	deleterious(ENST00000513005, ENST00000507069, ENST00000515082, ENST00000507460, ENST00000510233, ENST00000506961, ENST00000356504, ENST00000514090, ENST00000630416, ENST00000381620, ENST00000503806, ENST00000510861, ENST00000514193)
PolyPhen Annotation	probably_damaging
PolyPhen Variant Effect	probably_damaging(ENST00000513005, ENST00000507069, ENST00000515082, ENST00000507460, ENST00000510233, ENST00000506961, ENST00000356504, ENST00000514090, ENST00000630416, ENST00000381620, ENST00000503806, ENST00000510861, ENST00000514193)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	n/a
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
Nievergelt, C. M.,2015	PTSD	In 2179 MRS subjects of European descent: P-value=0.024. In 2179 MRS subjects of European descent: P-value=0.024.	P-value is nominally significant (P-value<0.05). P-value is nominally significant (P-value<0.05).	Significant

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

Reference	Phenotype	Environment	Statistical Values	Author Comments	Marker's Category
Nievergelt, C. M.,2015	PTSD	Childhood trauma	In 2179 MRS subjects of European descent, gene and childhood...... In 2179 MRS subjects of European descent, gene and childhood trauma interaction: P-value<0.05. More...	It showed a non-significant interaction effect with childhoo...... It showed a non-significant interaction effect with childhood trauma on PTSD. More...	Non-significant

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
GABRA2	gamma-aminobutyric acid (GABA) A receptor, alpha 2	4p12	3(1/2/0)

SNPs in LD with rs148139959 (count: 0)

SNP related eQTL (count: 1)

Gene Symbol	Gene Existed in PTSDgene?	Tissue	Trans/Cis	Source
CRHR1-IT1	Yes	Adipose Subcutaneous	cis	GTEx