SNP Report

Basic Info

Name	rs242939 dbSNP Ensembl
Location	17:45818213 - 45818213(+)
Variant Seq	T
Ancestral Allele	T
Ref Seq	C
Minor Allele Frequence	0.113019
Annotation	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant
Variant Effect	downstream_gene_variant(ENST00000587305); intron_variant(ENST00000580955, ENST00000314537, ENST00000293493, ENST00000577353, ENST00000352855, ENST00000347197, ENST00000583888, ENST00000634876, ENST00000398285, ENST00000582766, ENST00000634540, ENST00000619154, ENST00000339069); NMD_transcript_variant(ENST00000580955, ENST00000347197, ENST00000583888); non_coding_transcript_variant(ENST00000634876, ENST00000582766)
SIFT Annotation	tolerated
SIFT Variant Effect	tolerated(ENST00000580955, ENST00000398285, ENST00000577353, ENST00000347197, ENST00000293493, ENST00000314537)
PolyPhen Annotation	benign
PolyPhen Variant Effect	benign(ENST00000580955, ENST00000398285, ENST00000577353, ENST00000347197, ENST00000293493, ENST00000314537)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	n/a
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=-0.19, t=-0.57, P-value=0.57 In EA sunsamples: B=-0.19, t=-0.57, P-value=0.57	Not associated with higher post-hurricane PTSD symptoms. Not associated with higher post-hurricane PTSD symptoms.	Non-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 rs242939 (count: 3)

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]
rs171441	upstream_gene_variant(ENST00000583888); intron_variant(ENST00000619154, ENST00000580955, ENST00000398285, ENST00000314537, ENST00000634540, ENST00000293493, ENST00000347197, ENST00000577353, ENST00000582766, ENST00000339069, ENST00000587305, ENST00000634876, ENST00000352855); NMD_transcript_variant(ENST00000580955, ENST00000347197); non_coding_transcript_variant(ENST00000582766, ENST00000587305, ENST00000634876)	1(0/1/0)	1.0000[EUR]; 0.8525[AMR]

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs171442	rs171441 rs242939	upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9701[EUR]; 0.8525[AMR]
rs242938	rs171441 rs242939	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0000[EUR]; 0.8885[AMR]

SNP related eQTL (count: 1)

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