SNP Report

Basic Info

Name	rs258747 dbSNP Ensembl
Location	5:143277248 - 143277248(+)
Variant Seq	G
Ancestral Allele	G
Ref Seq	A
Minor Allele Frequence	0.402756
Annotation	downstream_gene_variant
Variant Effect	downstream_gene_variant(ENST00000231509, ENST00000415690, ENST00000343796, ENST00000394464, ENST00000424646, ENST00000503201, ENST00000504572, ENST00000394466)
SIFT Annotation	tolerated
SIFT Variant Effect	tolerated(ENST00000378004, ENST00000418236, ENST00000443674, ENST00000274498)
PolyPhen Annotation	benign; possibly_damaging
PolyPhen Variant Effect	benign(ENST00000378004, ENST00000418236); possibly_damaging(ENST00000443674, ENST00000274498)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	n/a
Chromatin State	Weak transcription;Strong transcription;Enhancers
No. of Marker's Association Results	1 (Positive: 1; Negative: 0; Trend: 0)
Source	Literature

SNP related association results

Normal genetic study related association results (count: 1)

Reference	Phenotype	Statistical Values	Author Comments	Marker's Category
Lian, Y.,2014	PTSD	Logistic regression analysis (after adjusting for age): gen...... Logistic regression analysis (after adjusting for age): genotype (A/A, G/A, G/G): P-value=0.003; allele (A with G): P-value=0.001. More...	We demonstrated that the presence of GG and GA genotypes and...... We demonstrated that the presence of GG and GA genotypes and the G allele (rs258747) significantly reduced the risk of PTSD, while presence of the A allele and AA genotype was a positive factor with respect to disease risk. More...	Significant

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
NR3C1	nuclear receptor subfamily 3 group C member 1	5q31-q32	6(2/4/0)

SNPs in LD with rs258747 (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]
rs852980	rs258747	intron_variant; non_coding_transcript_variant	0.8160[ASN]
rs6191	rs258747	downstream_gene_variant; 3_prime_UTR_variant	0.8016[ASN]
rs864354	rs258747	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8502[ASN]
rs853183	rs258747	downstream_gene_variant; 3_prime_UTR_variant; intron_variant	0.8411[ASN]
rs33388	rs258747	intron_variant; non_coding_transcript_variant	0.8411[ASN]
rs852976	rs258747	intron_variant; non_coding_transcript_variant	0.8411[ASN]
rs853175	rs258747	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8656[ASN]
rs33383	rs258747	upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8245[ASN]
rs258763	rs258747	downstream_gene_variant	0.8411[ASN]

SNP related eQTL (count: 1)

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