SNP Report

Basic Info

Name	rs7691872 dbSNP Ensembl
Location	4:165944433 - 165944433(+)
Variant Seq	T
Ancestral Allele	G
Ref Seq	G
Minor Allele Frequence	0.124002
Annotation	intron_variant; NMD_transcript_variant
Variant Effect	intron_variant(ENST00000507499, ENST00000506144, ENST00000513213, ENST00000509505, ENST00000504560, ENST00000061240); NMD_transcript_variant(ENST00000509505, ENST00000504560)
SIFT Annotation	tolerated_-_low_confidence; deleterious_-_low_confidence; deleterious
SIFT Variant Effect	tolerated_-_low_confidence(ENST00000061240, ENST00000507499); deleterious_-_low_confidence(ENST00000504560, ENST00000513213); deleterious(ENST00000509505)
PolyPhen Annotation	benign; possibly_damaging
PolyPhen Variant Effect	benign(ENST00000504560, ENST00000061240, ENST00000507499); possibly_damaging(ENST00000513213, ENST00000509505)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	n/a
Chromatin State	Weak transcription
No. of Marker's Association Results	2 (Positive: 0; Negative: 1; Trend: 1)
Source	Literature

SNP related association results

Normal genetic study related association results (count: 2)

Reference	Phenotype	Statistical Values	Author Comments	Marker's Category
Xie, P.,2013	Lifetime PTSD	Whole Cohort of European Americans: in GWAS,P-value=2.22E-0...... Whole Cohort of European Americans: in GWAS,P-value=2.22E-06,in replication,P-value=2.30E-04,in combined, P-value=1.22E-07 More...	No significant signals was observed about this SNP. No significant signals was observed about this SNP.	Trend
Almli, L. M.,2014	PTSD symptoms (mPSS)	Linear regression, main effect P-value=0.26 Linear regression, main effect P-value=0.26	They did not replicate as main effects in associations with ...... They did not replicate as main effects in associations with PTSD symptoms in this study. More...	Non-significant

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

Reference	Phenotype	Environment	Statistical Values	Author Comments	Marker's Category
Almli, L. M.,2014	PTSD symptoms (mPSS)	Childhood trauma	Linear regression, GxE P-value(standard regression model)=0....... Linear regression, GxE P-value(standard regression model)=0.11, GxE P-value(adjusted with robust standard errors with R package geepack)=0.13. More...	We haven't found a significant genotype and environment inte...... We haven't found a significant genotype and environment interaction (G x E) with childhood trauma in our AA population. More...	Non-significant

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
TLL1	tolloid like 1	4q32.3	4(2/2/0)

SNPs in LD with rs7691872 (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]

rs1503292	intron_variant(ENST00000507499, ENST00000509505, ENST00000061240, ENST00000504560, ENST00000513213, ENST00000506144); NMD_transcript_variant(ENST00000509505, ENST00000504560)	2(0/1/1)	0.8160[EUR]
rs6812849	intron_variant(ENST00000504560, ENST00000509505, ENST00000061240, ENST00000513213, ENST00000506144, ENST00000507499); NMD_transcript_variant(ENST00000504560, ENST00000509505)	3(1/2/0)	0.8160[EUR]

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs7666893	rs7691872 rs6812849 rs1503292	intron_variant; NMD_transcript_variant	1.0000[EUR]; 0.9832[AFR]; 1.0000[AMR]
rs7681099	rs7691872 rs6812849 rs1503292	intron_variant; NMD_transcript_variant	0.8160[EUR]
rs10034635	rs7691872 rs6812849 rs1503292	intron_variant; NMD_transcript_variant	1.0000[EUR]
rs28439605	rs7691872 rs6812849 rs1503292	intron_variant; NMD_transcript_variant	0.8160[EUR]
rs1393852	rs7691872 rs6812849 rs1503292	intron_variant; NMD_transcript_variant	0.8160[EUR]
rs7680388	rs7691872 rs6812849 rs1503292	intron_variant; NMD_transcript_variant	0.8160[EUR]
rs56033583	rs7691872 rs6812849 rs1503292	intron_variant; NMD_transcript_variant	0.8160[EUR]
rs7666241	rs7691872 rs6812849 rs1503292	intron_variant; NMD_transcript_variant	0.8160[EUR]

SNP related eQTL (count: 1)

Gene Symbol	Gene Existed in PTSDgene?	Tissue	Trans/Cis	Source
CRHR1-IT1	Yes	Adipose Subcutaneous	cis	GTEx