SNP Report

Basic Info

Name	rs4916008 dbSNP Ensembl
Location	1:64852824 - 64852824(+)
Variant Seq	T
Ancestral Allele	T
Ref Seq	C
Minor Allele Frequence	0.167732
Annotation	upstream_gene_variant; intron_variant
Variant Effect	upstream_gene_variant(ENST00000465376); intron_variant(ENST00000342505)
SIFT Annotation	deleterious
SIFT Variant Effect	deleterious(ENST00000342505)
PolyPhen Annotation	benign
PolyPhen Variant Effect	benign(ENST00000342505)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	TF binding region
Chromatin State	Weak transcription;Strong transcription
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
Nievergelt, C. M.,2015	PTSD	In subjects of European: P-value=4.0E-06. In subjects of European: P-value=4.0E-06.	It met the threshold for suggestive evidence of association ...... It met the threshold for suggestive evidence of association (P-value<5E-06). More...	Trend

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

Reference	Phenotype	Environment	Statistical Values	Author Comments	Marker's Category
Nievergelt, C. M.,2015	PTSD	Childhood trauma	Gene and childhood trauma interaction: P-value<0.05 in any s...... Gene and childhood trauma interaction: P-value<0.05 in any subjects. More...	It showed a non-significant interaction effect with childhoo...... It showed a non-significant interaction effect with childhood trauma on PTSD. More...	Non-significant

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
JAK1	Janus kinase 1	1p32.3-p31.3	1(0/0/1)

SNPs in LD with rs4916008 (count: 12)

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]
rs72920202	rs4916008	intron_variant	0.8444[EUR]; 0.8233[AMR]
rs2230587	rs4916008	synonymous_variant; non_coding_transcript_exon_variant; upstream_gene_variant; non_coding_transcript_variant	0.9634[EUR]; 0.9284[AMR]
rs17127117	rs4916008	downstream_gene_variant; intron_variant	0.9036[EUR]; 0.8934[AMR]
rs3790535	rs4916008	upstream_gene_variant; intron_variant	0.9634[EUR]; 1.0000[AFR]; 1.0000[AMR]
rs3790541	rs4916008	downstream_gene_variant; intron_variant	0.9152[EUR]; 0.8934[AMR]
rs17127090	rs4916008	upstream_gene_variant; intron_variant	0.9756[EUR]; 0.9468[AMR]
rs4916003	rs4916008	downstream_gene_variant; intron_variant	0.9394[EUR]; 0.8773[AMR]
rs7540450	rs4916008	intron_variant; NMD_transcript_variant	0.8088[EUR]
rs12406400	rs4916008	intron_variant; non_coding_transcript_variant	0.9391[EUR]; 0.9468[AMR]
rs3762311	rs4916008	intron_variant	0.8911[EUR]; 0.8233[AMR]
rs2274947	rs4916008	upstream_gene_variant; intron_variant	0.9152[EUR]; 0.8934[AMR]
rs55869683	rs4916008	downstream_gene_variant; intron_variant	0.9152[EUR]; 0.8934[AMR]

SNP related eQTL (count: 1)

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