SNP Report

Basic Info

Name	rs10002308 dbSNP Ensembl
Location	4:168478672 - 168478672(+)
Variant Seq	A
Ancestral Allele	A
Ref Seq	C
Minor Allele Frequence	0.389976
Annotation	intron_variant; non_coding_transcript_variant
Variant Effect	intron_variant(ENST00000511577, ENST00000515088, ENST00000260184, ENST00000514748, ENST00000512371, ENST00000505696, ENST00000513901, ENST00000505890, ENST00000505150); non_coding_transcript_variant(ENST00000515088, ENST00000513901, ENST00000505150)
SIFT Annotation	deleterious
SIFT Variant Effect	deleterious(ENST00000512371, ENST00000505696, ENST00000514748, ENST00000511577, ENST00000505890, ENST00000260184)
PolyPhen Annotation	probably_damaging
PolyPhen Variant Effect	probably_damaging(ENST00000512371, ENST00000505696, ENST00000514748, ENST00000511577, ENST00000505890, ENST00000260184)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	n/a
Chromatin State	Weak transcription;Active TSS;Enhancers;Flanking Active TSS;Genic enhancers
No. of Marker's Association Results	1 (Positive: 0; Negative: 0; Trend: 1)
Source	Literature

SNP related association results

Normal genetic study related association results (count: 1)

Reference	Phenotype	Statistical Values	Author Comments	Marker's Category
Ashley-Koch, A. E.,2015	Current PTSD	In meta-analysis: main effect P-value=1.67E-05. In meta-analysis: main effect P-value=1.67E-05.	This SNP was nominally significant with current PTSD after m...... This SNP was nominally significant with current PTSD after mete-analysis of NHB and NHW subset (P-value More...	Trend

G*E study related association result (count: 2)

Reference	Phenotype	Environment	Statistical Values	Author Comments	Marker's Category
Ashley-Koch, A. E.,2015	Current PTSD	Childhood trauma	Logistic regression (additive genetic model) in NHB subset: ...... Logistic regression (additive genetic model) in NHB subset: snp and child trauma interaction P-value=0.39; in NHW subset: snp and child trauma interaction P-value=0.046. More...	Among the NHW, we observed nominally significant interaction...... Among the NHW, we observed nominally significant interactions with childhood trauma for DDX60L. More...	Non-significant
Ashley-Koch, A. E.,2015	Current PTSD	NTE (number of traumatic events)	Logistic regression (additive genetic model) in NHB subset: ...... Logistic regression (additive genetic model) in NHB subset: snp and total trauma interaction P-value=0.88; in NHW subset: snp and total trauma interaction P-value=0.01. More...	The interaction between the total number of traumatic events...... The interaction between the total number of traumatic events and DDX60L in the NHW subset was nominally significant, consistent with the interaction observation with childhood trauma. More...	Non-significant

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
DDX60L	DEAD-box helicase 60-like	4q32.3	1(0/0/1)

SNPs in LD with rs10002308 (count: 9)

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	Literature-origin SNPs with LD	Annotation	r²[population]
rs55764504	rs10002308	intron_variant; non_coding_transcript_variant	0.8215[EUR]; 0.8339[AMR]
rs9999142	rs10002308	intron_variant; non_coding_transcript_variant	0.8272[EUR]
rs28675009	rs10002308	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.9489[EUR]; 0.8690[AFR]; 0.9735[AMR]
rs2710832	rs10002308	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.9658[EUR]; 0.8527[AFR]; 0.9472[AMR]
rs2710831	rs10002308	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.9658[EUR]; 0.8770[AFR]; 0.9472[AMR]
rs28524000	rs10002308	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.9489[EUR]; 0.9346[AMR]
rs12331721	rs10002308	intron_variant; non_coding_transcript_variant	0.8374[EUR]; 0.8461[AMR]
rs17054232	rs10002308	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8098[AMR]
rs13353710	rs10002308	intron_variant; non_coding_transcript_variant	0.9771[EUR]; 0.9838[AFR]; 1.0000[AMR]

SNP related eQTL (count: 1)

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