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.

rs_ID	Annotation	No. of Association Results(Positive/Negative/Trend)	r²[population]

rs10800465	downstream_gene_variant(ENST00000516453); upstream_gene_variant(ENST00000384996); intron_variant(ENST00000530878, ENST00000430120, ENST00000361897); NMD_transcript_variant(ENST00000430120)	1(0/1/0)	0.9935[EUR]

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs12043535	rs1858232 rs10800465	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant	0.9935[EUR]
rs1508264	rs1858232 rs10800465	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant	0.9935[EUR]
rs10919200	rs1858232 rs10800465	upstream_gene_variant; intron_variant; NMD_transcript_variant	1.0000[EUR]
rs10800464	rs1858232 rs10800465	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant	0.9935[EUR]
rs10753790	rs1858232 rs10800465	upstream_gene_variant; intron_variant; NMD_transcript_variant	0.9869[EUR]
rs12048687	rs1858232 rs10800465	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant	0.9935[EUR]
rs7544809	rs1858232 rs10800465	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.9546[EUR]
rs11587950	rs1858232 rs10800465	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant	0.9935[EUR]
rs3751285	rs1858232 rs10800465	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.9739[EUR]
rs11587952	rs1858232 rs10800465	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant	0.9935[EUR]

SNP related eQTL (count: 1)

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