SNP Report

Basic Info

Name	rs16940686 dbSNP Ensembl
Location	17:45835664 - 45835664(+)
Variant Seq	T
Ancestral Allele	G
Ref Seq	G
Minor Allele Frequence	0.0309505
Annotation	downstream_gene_variant; 3_prime_UTR_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant
Variant Effect	downstream_gene_variant(ENST00000580876, ENST00000535778, ENST00000577353, ENST00000581479, ENST00000582766, ENST00000352855, ENST00000583888); 3_prime_UTR_variant(ENST00000619154, ENST00000634540, ENST00000398285, ENST00000314537, ENST00000339069, ENST00000347197, ENST00000293493); intron_variant(ENST00000634876); NMD_transcript_variant(ENST00000347197); non_coding_transcript_variant(ENST00000634876)
SIFT Annotation	deleterious
SIFT Variant Effect	deleterious(ENST00000329196)
PolyPhen Annotation	probably_damaging
PolyPhen Variant Effect	probably_damaging(ENST00000329196)
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
White, S.,2013	Post-hurricane PTSD symptoms	In EA sunsamples: B=0.04, t=0.81, P-value=0.42 In EA sunsamples: B=0.04, t=0.81, P-value=0.42	Not associated with higher post-hurricane PTSD symptoms. Not associated with higher post-hurricane PTSD symptoms.	Non-significant

SNP related genes (count: 3)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
CRHR1	corticotropin releasing hormone receptor 1	17q21.31	12(6/6/0)
SPPL2C	signal peptide peptidase like 2C	17q21.31	Mapped by Literature SNP, Mapped by LD-proxy, rSNP target
MAPT-AS1	MAPT antisense RNA 1	17q21.31	Mapped by Literature SNP, Mapped by LD-proxy, rSNP target

SNPs in LD with rs16940686 (count: 14)

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: 0)

LD-proxies (count: 14)

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs12952224	rs16940686	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9204[AMR]
rs35327015	rs16940686	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8513[EUR]; 1.0000[AMR]
rs36048893	rs16940686	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8513[EUR]; 1.0000[AMR]
rs16940704	rs16940686	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.9308[EUR]; 1.0000[AFR]
rs12939006	rs16940686	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9204[AMR]
rs71375321	rs16940686	upstream_gene_variant; 3_prime_UTR_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8513[EUR]; 1.0000[AMR]
rs34845889	rs16940686	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8973[EUR]
rs5820597	rs16940686	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0000[EUR]; 0.9204[AMR]
rs36069290	rs16940686	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9204[AMR]
rs12937956	rs16940686	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0000[EUR]; 1.0000[AFR]; 1.0000[AMR]
rs3785877	rs16940686	upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8173[EUR]; 1.0000[AMR]
rs16940711	rs16940686	intron_variant; non_coding_transcript_variant	0.8963[EUR]; 1.0000[AFR]
rs28364027	rs16940686	downstream_gene_variant; 3_prime_UTR_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0000[EUR]; 1.0000[AFR]; 1.0000[AMR]
rs12936511	rs16940686	synonymous_variant; non_coding_transcript_exon_variant; 5_prime_UTR_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9204[AMR]

SNP related eQTL (count: 1)

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