PTSDgene database

SNP Report

Basic Info
Name rs1143643 dbSNP Ensembl
Location 2:112830725 - 112830725(+)
Variant Seq T
Ancestral Allele C
Ref Seq C
Minor Allele Frequence 0.28774
Annotation downstream_gene_variant; intron_variant; non_coding_transcript_variant
Variant Effect downstream_gene_variant(ENST00000432018, ENST00000416750, ENST00000418817, ENST00000477398, ENST00000496280, ENST00000487639); intron_variant(ENST00000263341, ENST00000491056); non_coding_transcript_variant(ENST00000491056)
SIFT Annotation tolerated
SIFT Variant Effect tolerated(ENST00000263341)
PolyPhen Annotation probably_damaging
PolyPhen Variant Effect probably_damaging(ENST00000263341)
rSNP? Yes Link in rVarBase
Related Regulatory Elements Chromatin interactive region
Chromatin State Weak transcription;Strong transcription;Genic enhancers;Transcr. at gene 5' nd 3'
No. of Marker's Association Results 1 (Positive: 0; Negative: 1; 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
Hovhannisyan, L.,2017 PTSD diagnosis T carriage: OR=0.98, P-value=1, corrected P-value=1. T carriage: OR=0.98, P-value=1, corrected P-value=1. No association between this SNP and PTSD was found. No association between this SNP and PTSD was found. Non-significant

SNP related genes (count: 1)
Approved Symbol Approved Name Location No. of Association Results (Positive/Negative/Trend)
IL1B interleukin 1 beta 2q14 1(1/0/0)

SNPs in LD with rs1143643 (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: 1)

LD-proxies (count: 2)

SNP related eQTL (count: 1)
Gene Symbol Gene Existed in PTSDgene? Tissue Trans/Cis Source
RP11-707O23.5 No Adipose Subcutaneous cis GTEx