PTSDgene database

Pathway Enrichment Analysis Protein-Protein Interaction Analysis

SNP Report

Basic Info

Name	rs1878399 dbSNP Ensembl
Location	15:78619661 - 78619661(+)
Variant Seq	C
Ancestral Allele	C
Ref Seq	G
Minor Allele Frequence	0.268371
Annotation	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant
Variant Effect	downstream_gene_variant(ENST00000412074, ENST00000261751); upstream_gene_variant(ENST00000559080); intron_variant(ENST00000559658, ENST00000326828, ENST00000561128, ENST00000348639, ENST00000559941); NMD_transcript_variant(ENST00000559658); non_coding_transcript_variant(ENST00000561128, ENST00000559941)
SIFT Annotation	tolerated
SIFT Variant Effect	tolerated(ENST00000348639, ENST00000326828, ENST00000559658)
PolyPhen Annotation	benign
PolyPhen Variant Effect	benign(ENST00000348639, ENST00000326828, ENST00000559658)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	TF binding region;Chromatin interactive region
Chromatin State	Bivalent/Poised TSS;Flanking Bivalent TSS/Enh;Enhancers;Bivalent Enhancer;Flanking Active TSS;Active TSS
No. of Marker's Association Results	0 (Positive: 0; Negative: 0; Trend: 0)
Source	LD-proxy

SNP related association results

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)
CHRNB4	cholinergic receptor, nicotinic beta 4	15q24	Mapped by Literature SNP, Mapped by LD-proxy, rSNP target

SNPs in LD with rs1878399 (count: 0)

SNP related eQTL (count: 1)

Gene Symbol	Gene Existed in PTSDgene?	Tissue	Trans/Cis	Source
RP11-259G18.3	No	Adipose Subcutaneous	cis	GTEx