PTSDgene database

SNP Report

Basic Info
Name rs28932171 dbSNP Ensembl
Location 10:60071532 - 60071532(+)
Variant Seq C
Ancestral Allele T
Ref Seq T
Minor Allele Frequence 0.0315495
Annotation missense_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant
Variant Effect missense_variant(ENST00000621739, ENST00000280772); upstream_gene_variant(ENST00000610901, ENST00000613207); intron_variant(ENST00000610321, ENST00000616444, ENST00000511043, ENST00000503366, ENST00000618374, ENST00000373827, ENST00000373820, ENST00000355288); NMD_transcript_variant(ENST00000621739)
SIFT Annotation tolerated_-_low_confidence; tolerated
SIFT Variant Effect tolerated_-_low_confidence(ENST00000280772); tolerated(ENST00000621739)
PolyPhen Annotation benign
PolyPhen Variant Effect benign(ENST00000621739, ENST00000280772)
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
Logue, M. W.,2013 PTSD OR=0.48, P-value=0.00060, corrected P-value=0.045 OR=0.48, P-value=0.00060, corrected P-value=0.045 The SNP was associated with PTSD at the P-value<0.01 level. The SNP was associated with PTSD at the P-value<0.01 level. Significant

SNP related genes (count: 1)
Approved Symbol Approved Name Location No. of Association Results (Positive/Negative/Trend)
ANK3 ankyrin 3, node of Ranvier (ankyrin G) 10q21 2(2/0/0)

SNPs in LD with rs28932171 (count: 14)
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: 3)

LD-proxies (count: 11)

SNP related eQTL (count: 1)
Gene Symbol Gene Existed in PTSDgene? Tissue Trans/Cis Source
RP11-259G18.3 No Adipose Subcutaneous cis GTEx