SNP Report

Basic Info

Name	rs242924 dbSNP Ensembl
Location	17:45808001 - 45808001(+)
Variant Seq	T
Ancestral Allele	G
Ref Seq	G
Minor Allele Frequence	0.436302
Annotation	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
Variant Effect	intron_variant(ENST00000577353, ENST00000339069, ENST00000398285, ENST00000582766, ENST00000634876, ENST00000352855, ENST00000634540, ENST00000619154, ENST00000580955, ENST00000587305, ENST00000347197, ENST00000293493, ENST00000314537); NMD_transcript_variant(ENST00000580955, ENST00000347197); non_coding_transcript_variant(ENST00000582766, ENST00000634876, ENST00000587305)
SIFT Annotation	tolerated
SIFT Variant Effect	tolerated(ENST00000293493, ENST00000398285, ENST00000314537, ENST00000577353, ENST00000347197, ENST00000580955)
PolyPhen Annotation	benign; possibly_damaging
PolyPhen Variant Effect	benign(ENST00000293493, ENST00000398285, ENST00000314537, ENST00000577353); possibly_damaging(ENST00000347197, ENST00000580955)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	n/a
Chromatin State	Weak transcription
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
White, S.,2013	Post-hurricane PTSD symptoms	In EA sunsamples: B=-0.40, t=-1.62, P-value=0.11 In EA sunsamples: B=-0.40, t=-1.62, P-value=0.11	Not associated with higher post-hurricane PTSD symptoms. Not associated with higher post-hurricane PTSD symptoms.	Non-significant
Binder, E. B.,2008	PTSD symptom severity	No available detail information. No available detail information.	It showed a non-significant main effect on PTSD symptom seve...... It showed a non-significant main effect on PTSD symptom severity. More...	Non-significant

G*E study related association result (count: 1)

Reference	Phenotype	Environment	Statistical Values	Author Comments	Marker's Category
Binder, E. B.,2008	PTSD Symptom Severity	Child abuse	No available detail information. No available detail information.	It showed a non-significant interaction effect with child ab...... It showed a non-significant interaction effect with child abuse or non-child abuse trauma exposure on PTSD symptom severity. More...	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 rs242924 (count: 10)

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]

rs4074461	intron_variant(ENST00000634540, ENST00000587305); non_coding_transcript_variant(ENST00000587305)	1(1/0/0)	0.8345[EUR]
rs110402	upstream_gene_variant(ENST00000580955); intron_variant(ENST00000352855, ENST00000619154, ENST00000582766, ENST00000634876, ENST00000587305, ENST00000634540, ENST00000398285, ENST00000314537, ENST00000347197, ENST00000577353, ENST00000293493, ENST00000339069); NMD_transcript_variant(ENST00000347197); non_coding_transcript_variant(ENST00000582766, ENST00000634876, ENST00000587305)	2(0/2/0)	0.9737[EUR]; 1.0000[AMR]
rs7209436	intron_variant(ENST00000293493, ENST00000619154, ENST00000314537, ENST00000398285, ENST00000352855, ENST00000582766, ENST00000587305, ENST00000634540, ENST00000347197, ENST00000577353, ENST00000339069); NMD_transcript_variant(ENST00000347197); non_coding_transcript_variant(ENST00000582766, ENST00000587305)	2(0/2/0)	0.8934[EUR]; 0.9674[AMR]

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs242925	rs7209436 rs242924 rs110402	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8554[EUR]; 0.9485[AFR]; 0.9568[AMR]
rs12952301	rs4074461 rs7209436 rs242924 rs110402	intron_variant; non_coding_transcript_variant	0.8392[EUR]; 0.8319[AMR]
rs81189	rs7209436 rs242924 rs110402	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8268[EUR]; 0.9140[AMR]
rs242949	rs242924 rs110402	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8111[AMR]
rs12950522	rs4074461 rs7209436 rs242924 rs110402	upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8446[EUR]; 0.8529[AMR]
rs171440	rs7209436 rs242924 rs110402	upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8410[EUR]; 0.9256[AMR]
rs242940	rs7209436 rs242924 rs110402	upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8416[EUR]; 0.9358[AMR]

SNP related eQTL (count: 1)

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