SNP Report

Basic Info

Name	rs41423247 dbSNP Ensembl
Location	5:143399010 - 143399010(+)
Variant Seq	C
Ancestral Allele	G
Ref Seq	G
Minor Allele Frequence	0.254593
Annotation	downstream_gene_variant; intron_variant
Variant Effect	downstream_gene_variant(ENST00000502892, ENST00000502500, ENST00000510170, ENST00000508760, ENST00000514699); intron_variant(ENST00000343796, ENST00000504572, ENST00000503201, ENST00000394466, ENST00000231509, ENST00000415690, ENST00000394464, ENST00000424646)
SIFT Annotation	tolerated_-_low_confidence; tolerated
SIFT Variant Effect	tolerated_-_low_confidence(ENST00000504572, ENST00000394464, ENST00000424646, ENST00000394466, ENST00000231509, ENST00000503201, ENST00000415690, ENST00000343796); tolerated(ENST00000510170, ENST00000502892, ENST00000502500, ENST00000514699, ENST00000508760)
PolyPhen Annotation	benign
PolyPhen Variant Effect	benign(ENST00000504572, ENST00000394464, ENST00000424646, ENST00000510170, ENST00000502892, ENST00000502500, ENST00000514699, ENST00000394466, ENST00000231509, ENST00000503201, ENST00000415690, ENST00000508760, ENST00000343796)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	Chromatin interactive region
Chromatin State	Enhancers;Active TSS;Flanking Active TSS;Weak transcription;Transcr. at gene 5' nd 3';Genic enhancers;Bivalent/Poised TSS;Strong transcription
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 (C/C, C/G, G/G): P-value=0.004; allele (C with G): P-value=0.003, OR=1.29, 95%CI=1.09-1.54. More...	Subjects with the G allele and CG genotype (rs41423247) had ...... Subjects with the G allele and CG genotype (rs41423247) had an increased likelihood of PTSD compared with those with the C allele and CC genotype. More...	Significant

SNP related genes (count: 2)

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)
ARHGAP26	Rho GTPase activating protein 26	5q31	rSNP target

SNPs in LD with rs41423247 (count: 3)

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]
rs7716360	rs41423247	intron_variant; non_coding_transcript_variant	0.8084[ASN]
rs10041520	rs41423247	downstream_gene_variant; intron_variant	0.8084[ASN]
rs258762	rs41423247	downstream_gene_variant; 3_prime_UTR_variant	0.8303[ASN]

SNP related eQTL (count: 1)

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