PTSDgene database

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.

Literature-origin SNPs (count: 0)

LD-proxies (count: 3)

SNP related eQTL (count: 1)
Gene Symbol Gene Existed in PTSDgene? Tissue Trans/Cis Source
CRHR1-IT1 Yes Adipose Subcutaneous cis GTEx