PTSDgene database

SNP Report

Basic Info
Name rs1858232 dbSNP Ensembl
Location 1:162334048 - 162334048(+)
Variant Seq G
Ancestral Allele A
Ref Seq A
Minor Allele Frequence 0.331869
Annotation upstream_gene_variant; intron_variant; NMD_transcript_variant
Variant Effect upstream_gene_variant(ENST00000516453); intron_variant(ENST00000430120, ENST00000361897, ENST00000530878); NMD_transcript_variant(ENST00000430120)
SIFT Annotation deleterious
SIFT Variant Effect deleterious(ENST00000361897, ENST00000430120, ENST00000530878)
PolyPhen Annotation probably_damaging
PolyPhen Variant Effect probably_damaging(ENST00000361897, ENST00000430120, ENST00000530878)
rSNP? Yes Link in rVarBase
Related Regulatory Elements Chromatin interactive region
Chromatin State Weak transcription;Enhancers;Strong 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
Lawford, B. R.,2013 PTSD Allele frequencies: X2=1.078, P-value=0.299, OR=...... Allele frequencies: X2=1.078, P-value=0.299, OR=1.18, 95%CI(0.61-1.18). More... No significant signals was observed about this SNP. No significant signals was observed about this SNP. Non-significant


SNP related genes (count: 4)
Approved Symbol Approved Name Location No. of Association Results (Positive/Negative/Trend)
MIR556 microRNA 556 1q23.3 Mapped by Literature SNP, Mapped by LD-proxy, rSNP target
NOS1AP nitric oxide synthase 1 adaptor protein 1q23.3 3(3/0/0)
RNA5SP61 RNA, 5S ribosomal pseudogene 61 1q23.3 Mapped by Literature SNP, Mapped by LD-proxy, rSNP target
UAP1 UDP-N-acetylglucosamine pyrophosphorylase 1 1q23.2 rSNP target

SNPs in LD with rs1858232 (count: 11)
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: 10)


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