PTSDgene database

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