SNP Report

Basic Info

Name	rs406001 dbSNP Ensembl
Location	7:51938719 - 51938719(+)
Variant Seq	C
Ancestral Allele	T
Ref Seq	T
Minor Allele Frequence	0.0712859
Annotation	downstream_gene_variant
SIFT Annotation	deleterious_-_low_confidence; tolerated
SIFT Variant Effect	deleterious_-_low_confidence(ENST00000395540); tolerated(ENST00000632460, ENST00000265136, ENST00000441453, ENST00000395542)
PolyPhen Annotation	benign; possibly_damaging
PolyPhen Variant Effect	benign(ENST00000441453); possibly_damaging(ENST00000632460, ENST00000395540, ENST00000265136, ENST00000395542)
rSNP?	No Link in rVarBase
Related Regulatory Elements	n/a
Chromatin State	Inactive region
No. of Marker's Association Results	2 (Positive: 1; Negative: 1; 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
Xie, P.,2013	Lifetime PTSD	Whole Cohort of European Americans: in GWAS,P-value=3.97E-0...... Whole Cohort of European Americans: in GWAS,P-value=3.97E-08,in replication,P-value=0.95,in combined, P-value=2.77E-04;Trauma Exposed European Americans: in GWAS,P-value=1.14E-07,in replication,P-value=0.41,in combined, P-value=3.41E-03. More...	In EAs,they observed that one SNP on chromosome 7p12, rs4060...... In EAs,they observed that one SNP on chromosome 7p12, rs406001, exceeded genome-wide significance. More...	Significant
Almli, L. M.,2014	PTSD symptoms (mPSS)	Linear regression, main effect P-value=0.34 Linear regression, main effect P-value=0.34	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)=0.0006, GxE P-value(adjusted with robust standard errors with R package geepack)=0.002. More...	We found a significant genotype and environment interaction ...... We found a significant genotype and environment interaction (G x E) with childhood trauma in our AA population. More...	Significant

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
COBL	cordon-bleu WH2 repeat protein	7p12.2-p12.1	2(1/1/0)

SNPs in LD with rs406001 (count: 35)

The LD data used here is based on 1000 Genome Phase I. LD SNP pairs were selected with a threshold r²<=0.8.

Literature-origin SNPs (count: 1)

rs_ID	Annotation	No. of Association Results(Positive/Negative/Trend)	r²[population]

rs382903		2(0/1/1)	1.0000[EUR]

LD-proxies (count: 34)

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs400204	rs406001 rs382903	downstream_gene_variant	0.8322[EUR]
rs438867	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]; 0.8504[AFR]; 0.8773[AMR]
rs377851	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]; 0.8617[AMR]
rs454404	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]; 0.9313[AFR]; 0.9348[AMR]
rs10480946	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]
rs411093	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]; 0.8504[AFR]; 0.8773[AMR]
rs410473	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]; 0.9307[AMR]
rs608826	rs406001 rs382903	downstream_gene_variant	0.8319[AFR]; 0.8773[AMR]
rs616199	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]; 0.8657[AMR]
rs647653	rs406001 rs382903	downstream_gene_variant	0.8560[EUR]
rs455017	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]; 0.9313[AFR]; 0.9348[AMR]
rs382727	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]; 0.8504[AFR]; 0.8773[AMR]
rs364752	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]
rs396471	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]; 0.8504[AFR]; 0.8773[AMR]
rs413648	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]; 0.8032[AFR]; 0.8657[AMR]
rs10265236	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]; 0.8089[AMR]
rs384551	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]; 0.8504[AFR]; 0.8773[AMR]
rs379235	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]; 0.8504[AFR]; 0.8773[AMR]
rs10234957	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]; 0.8835[AFR]; 0.9307[AMR]
rs6971505	rs406001 rs382903	downstream_gene_variant	0.8322[EUR]
rs408595	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]; 0.8504[AFR]; 0.8773[AMR]
rs392252	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]
rs424283	rs406001 rs382903	downstream_gene_variant	0.8322[EUR]
rs426522	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]; 0.8504[AFR]; 0.8773[AMR]
rs428360	rs406001 rs382903	downstream_gene_variant	0.8657[AMR]
rs590600	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]; 0.8140[AFR]; 0.8773[AMR]
rs409776	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]; 0.8504[AFR]; 0.8773[AMR]
rs417388	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]
rs664926	rs406001 rs382903	downstream_gene_variant	0.8560[EUR]
rs411481	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]; 0.8504[AFR]; 0.8773[AMR]
rs403531	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]; 0.9521[AFR]; 1.0000[AMR]
rs454526	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]
rs402450	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]; 0.8504[AFR]; 0.8773[AMR]
rs452777	rs406001 rs382903	downstream_gene_variant	1.0000[EUR]; 0.8319[AFR]; 0.8261[AMR]

SNP related eQTL (count: 1)

Gene Symbol	Gene Existed in PTSDgene?	Tissue	Trans/Cis	Source
LRRC37A4P	No	Adipose Subcutaneous	cis	GTEx