SNP Report

Basic Info

Name	rs17689966 dbSNP Ensembl
Location	17:45833089 - 45833089(+)
Variant Seq	A
Ancestral Allele	G
Ref Seq	G
Minor Allele Frequence	0.360224
Annotation	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant
Variant Effect	downstream_gene_variant(ENST00000580955, ENST00000582766); upstream_gene_variant(ENST00000535778, ENST00000580876); intron_variant(ENST00000583888, ENST00000619154, ENST00000398285, ENST00000634540, ENST00000634876, ENST00000581479, ENST00000293493, ENST00000352855, ENST00000339069, ENST00000314537, ENST00000347197, ENST00000577353); NMD_transcript_variant(ENST00000583888, ENST00000347197); non_coding_transcript_variant(ENST00000634876, ENST00000581479)
SIFT Annotation	deleterious_-_low_confidence; deleterious
SIFT Variant Effect	deleterious_-_low_confidence(ENST00000535778); deleterious(ENST00000577353, ENST00000314537, ENST00000398285, ENST00000293493, ENST00000634540, ENST00000352855, ENST00000339069)
PolyPhen Annotation	benign; probably_damaging
PolyPhen Variant Effect	benign(ENST00000535778); probably_damaging(ENST00000577353, ENST00000314537, ENST00000398285, ENST00000293493, ENST00000634540, ENST00000352855, ENST00000339069)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	TF binding region
Chromatin State	Weak transcription
No. of Marker's Association Results	1 (Positive: 1; Negative: 0; 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
White, S.,2013	Post-hurricane PTSD symptoms	In EA sunsamples: B=0.76, t=1.98, P-value=0.049 In EA sunsamples: B=0.76, t=1.98, P-value=0.049	Nominally associated with higher post-hurricane PTSD symptom...... Nominally associated with higher post-hurricane PTSD symptoms More...	Significant

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
CRHR1	corticotropin releasing hormone receptor 1	17q21.31	12(6/6/0)
MAPT-AS1	MAPT antisense RNA 1	17q21.31	Mapped by Literature SNP, Mapped by LD-proxy, rSNP target

SNPs in LD with rs17689966 (count: 6)

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]
rs173365	intron_variant(ENST00000293493, ENST00000583888, ENST00000352855, ENST00000398285, ENST00000619154, ENST00000339069, ENST00000314537, ENST00000580955, ENST00000347197, ENST00000577353, ENST00000634540, ENST00000634876, ENST00000582766); NMD_transcript_variant(ENST00000583888, ENST00000580955, ENST00000347197); non_coding_transcript_variant(ENST00000634876, ENST00000582766)	1(1/0/0)	0.9946[EUR]; 0.9441[AMR]

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs242947	rs173365 rs17689966	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.9946[EUR]; 0.9227[AMR]
rs242944	rs173365 rs17689966	missense_variant; upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.9946[EUR]; 0.9227[AMR]
rs242948	rs173365 rs17689966	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.9893[EUR]; 0.9334[AMR]
rs242951	rs173365 rs17689966	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9893[EUR]; 0.9441[AMR]
rs242937	rs173365 rs17689966	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9946[EUR]; 0.9441[AMR]

SNP related eQTL (count: 1)

Gene Symbol	Gene Existed in PTSDgene?	Tissue	Trans/Cis	Source
DND1P1	No	Adipose Subcutaneous	cis	GTEx