PTSDgene database

SNP Report

Basic Info
Name rs1799913 dbSNP Ensembl
Location 11:18025708 - 18025708(+)
Variant Seq A,T
Ancestral Allele T
Ref Seq G
Minor Allele Frequence 0.321086
Annotation downstream_gene_variant; upstream_gene_variant; intron_variant; splice_region_variant; NMD_transcript_variant
Variant Effect downstream_gene_variant(ENST00000528338); upstream_gene_variant(ENST00000525523, ENST00000525406); intron_variant(ENST00000417164, ENST00000250018); splice_region_variant(ENST00000417164, ENST00000250018); NMD_transcript_variant(ENST00000417164)
SIFT Annotation tolerated
SIFT Variant Effect tolerated(ENST00000265965, ENST00000525422, ENST00000528200)
PolyPhen Annotation unknown; benign
PolyPhen Variant Effect unknown(ENST00000524716); benign(ENST00000265965, ENST00000525422, ENST00000528200)
rSNP? Yes Link in rVarBase
Related Regulatory Elements Chromatin interactive region
Chromatin State Weak transcription
No. of Marker's Association Results 1 (Positive: 0; Negative: 1; 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
Goenjian, A. K.,2012 PTSD-RI (PTSD symptoms) After adjusting for age, sex, exposure and environmental var...... After adjusting for age, sex, exposure and environmental variables, the family based variance component analyses of PTSD-RI with rs1799913: P-value=0.69, lod score=0.56. More... No significant association was observed. No significant association was observed. Non-significant

SNP related genes (count: 2)
Approved Symbol Approved Name Location No. of Association Results (Positive/Negative/Trend)
SERGEF secretion regulating guanine nucleotide exchange factor 11p14.3 Mapped by LD-proxy, rSNP target
TPH1 tryptophan hydroxylase 1 11p15.3-p14 5(1/4/0)

SNPs in LD with rs1799913 (count: 46)
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: 1)

LD-proxies (count: 45)

SNP related eQTL (count: 1)
Gene Symbol Gene Existed in PTSDgene? Tissue Trans/Cis Source
LRRC37A4P No Adipose Subcutaneous cis GTEx