SNP Report

Basic Info

Name	rs584007 dbSNP Ensembl
Location	19:44913221 - 44913221(+)
Variant Seq	G
Ref Seq	A
Minor Allele Frequence	0.402955
Annotation	downstream_gene_variant; non_coding_transcript_exon_variant; upstream_gene_variant; non_coding_transcript_variant
Variant Effect	downstream_gene_variant(ENST00000446996, ENST00000425718, ENST00000434152, ENST00000252486); non_coding_transcript_exon_variant(ENST00000623895); upstream_gene_variant(ENST00000592535, ENST00000586638, ENST00000589781, ENST00000588750, ENST00000590334, ENST00000588802, ENST00000592885, ENST00000592176, ENST00000589078); non_coding_transcript_variant(ENST00000623895)
SIFT Annotation	deleterious_-_low_confidence; deleterious
SIFT Variant Effect	deleterious_-_low_confidence(ENST00000592885, ENST00000586638); deleterious(ENST00000588750, ENST00000592535, ENST00000588802)
PolyPhen Annotation	unknown; benign; possibly_damaging
PolyPhen Variant Effect	unknown(ENST00000586638); benign(ENST00000588750, ENST00000592535, ENST00000588802); possibly_damaging(ENST00000592885)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	TF binding region;Chromatin interactive region
Chromatin State	Enhancers;Weak transcription;Flanking Active TSS;Bivalent Enhancer
No. of Marker's Association Results	2 (Positive: 0; Negative: 2; Trend: 0)
Source	Literature

SNP related association results

Normal genetic study related association results (count: 2)

Reference	Phenotype	Statistical Values	Author Comments	Marker's Category
Solovieff, N.,2014	PTSD diagnosis	P-value=0.066 P-value=0.066	Achieved nominal levels of significance with PTSD diagnosis,...... Achieved nominal levels of significance with PTSD diagnosis, although was not significant after correction for multiple testing More...	Non-significant
Solovieff, N.,2014	PTSD severity	P-value=0.020 P-value=0.020	Achieved nominal levels of significance with PTSD severity, ...... Achieved nominal levels of significance with PTSD severity, although was not significant after correction for multiple testing More...	Non-significant

SNP related genes (count: 4)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
APOE	apolipoprotein E	19q13.31	6(2/4/0)
APOC1	apolipoprotein C-I	19q13.2	Mapped by Literature SNP, Mapped by LD-proxy
PPP1R37	protein phosphatase 1 regulatory subunit 37	19q13.32	rSNP target
APOC4	apolipoprotein C-IV	19q13.2	rSNP target

SNPs in LD with rs584007 (count: 4)

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	Literature-origin SNPs with LD	Annotation	r²[population]
rs439401	rs584007	downstream_gene_variant; non_coding_transcript_exon_variant; upstream_gene_variant; non_coding_transcript_variant	0.9944[EUR]
rs157595	rs584007	downstream_gene_variant; upstream_gene_variant	0.8026[EUR]
rs3826688	rs584007	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.9347[EUR]
rs484195	rs584007	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.8334[EUR]

SNP related eQTL (count: 1)

Gene Symbol	Gene Existed in PTSDgene?	Tissue	Trans/Cis	Source
RP5-1109J22.1	No	Adipose Subcutaneous	cis	GTEx