SNP Report

Basic Info

Name	rs10457838 dbSNP Ensembl
Location	6:149036411 - 149036411(+)
Variant Seq	T
Ancestral Allele	C
Ref Seq	C
Minor Allele Frequence	0.228235
Annotation	upstream_gene_variant; intron_variant
Variant Effect	upstream_gene_variant(ENST00000433442); intron_variant(ENST00000367463)
SIFT Annotation	deleterious
SIFT Variant Effect	deleterious(ENST00000367463)
PolyPhen Annotation	possibly_damaging
PolyPhen Variant Effect	possibly_damaging(ENST00000367463)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	Chromatin interactive region
Chromatin State	Weak transcription;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
Nievergelt, C. M.,2015	PTSD	In subjects of African: P-value=2.2E-06. In subjects of African: P-value=2.2E-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)
UST	uronyl-2-sulfotransferase	6q25.1	1(0/0/1)

SNPs in LD with rs10457838 (count: 28)

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: 0)

LD-proxies (count: 28)

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs10782309	rs10457838	intron_variant	0.8943[EUR]
rs1934218	rs10457838	intron_variant; non_coding_transcript_variant	0.9337[EUR]; 0.8401[AMR]
rs12201653	rs10457838	intron_variant	0.9204[EUR]; 0.8826[AMR]
rs11967885	rs10457838	intron_variant	0.8688[EUR]
rs17732007	rs10457838	intron_variant; non_coding_transcript_variant	0.8623[EUR]; 0.8444[AMR]
rs10872632	rs10457838	intron_variant; non_coding_transcript_variant	0.8323[EUR]; 0.8444[AMR]
rs12211152	rs10457838	intron_variant	0.9078[EUR]; 0.8698[AMR]
rs62426150	rs10457838	downstream_gene_variant; intron_variant	0.9597[EUR]; 0.8033[AFR]; 0.9211[AMR]
rs62426156	rs10457838	intron_variant; non_coding_transcript_variant	0.8685[EUR]; 0.8444[AMR]
rs56358125	rs10457838	intron_variant	0.9148[EUR]; 0.9079[AMR]
rs17669693	rs10457838	intron_variant	0.9665[EUR]; 0.8826[AMR]
rs11759315	rs10457838	intron_variant	0.9598[EUR]; 0.9079[AMR]
rs2879862	rs10457838	intron_variant; non_coding_transcript_variant	0.8685[EUR]; 0.8444[AMR]
rs6938335	rs10457838	intron_variant; non_coding_transcript_variant	0.9597[EUR]; 0.9211[AMR]
rs9322164	rs10457838	intron_variant	0.9215[EUR]; 0.9209[AMR]
rs11155615	rs10457838	intron_variant	0.9535[EUR]; 0.8033[AMR]
rs10872630	rs10457838	upstream_gene_variant; intron_variant	0.8623[EUR]; 0.8444[AMR]
rs7772696	rs10457838	downstream_gene_variant	0.8130[EUR]
rs1934220	rs10457838	intron_variant	0.9598[EUR]; 0.9079[AMR]
rs4897078	rs10457838	downstream_gene_variant; 3_prime_UTR_variant	0.8130[EUR]
rs6932386	rs10457838	upstream_gene_variant; intron_variant	0.8685[EUR]; 0.8444[AMR]
rs58644381	rs10457838	intron_variant; non_coding_transcript_variant	0.8940[EUR]; 0.8319[AMR]
rs7756263	rs10457838	intron_variant; non_coding_transcript_variant	0.9531[EUR]; 0.8141[AFR]; 0.9343[AMR]
rs6903827	rs10457838	downstream_gene_variant	0.8317[EUR]
rs12205788	rs10457838	intron_variant	0.9072[EUR]
rs6939103	rs10457838	downstream_gene_variant	0.8562[EUR]
rs10872631	rs10457838	intron_variant; non_coding_transcript_variant	0.8685[EUR]; 0.8444[AMR]
rs4897077	rs10457838	intron_variant; non_coding_transcript_variant	0.8685[EUR]; 0.8197[AMR]

SNP related eQTL (count: 1)

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