PTSDgene database

SNP Report

Basic Info
Name rs60646603 dbSNP Ensembl
Location 8:27470188 - 27470188(+)
Variant Seq G
Ancestral Allele A
Ref Seq A
Minor Allele Frequence 0.00499201
Annotation downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant
Variant Effect downstream_gene_variant(ENST00000520650, ENST00000520208); upstream_gene_variant(ENST00000522008, ENST00000520600); intron_variant(ENST00000518712, ENST00000523695, ENST00000521921, ENST00000407991, ENST00000524096, ENST00000240132, ENST00000520933); NMD_transcript_variant(ENST00000523695)
SIFT Annotation deleterious
SIFT Variant Effect deleterious(ENST00000523695, ENST00000520933, ENST00000407991, ENST00000524096)
PolyPhen Annotation probably_damaging
PolyPhen Variant Effect probably_damaging(ENST00000523695, ENST00000520933, ENST00000407991, ENST00000524096)
rSNP? Yes Link in rVarBase
Related Regulatory Elements Chromatin interactive region
Chromatin State Weak 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
Kimbrel, N. A.,2015 PTSD In the NHB sample, main effect: P-value=0.03028. In the NHB sample, main effect: P-value=0.03028. Nominally significant associations (p<.05) were observed, bu...... Nominally significant associations (p<.05) were observed, but it didn't met multiple-testing threshold. More... Significant
G*E study related association result (count: 1)
Reference Phenotype Environment Statistical Values Author Comments Marker's Category
Kimbrel, N. A.,2015 PTSD Smoking status GxE interactions among NHB participants: P-value=0.7831. GxE interactions among NHB participants: P-value=0.7831. No GxE interactions were statistically significant among NHB...... No GxE interactions were statistically significant among NHB participants. More... Non-significant


SNP related genes (count: 2)
Approved Symbol Approved Name Location No. of Association Results (Positive/Negative/Trend)
CHRNA2 cholinergic receptor, nicotinic alpha 2 8p21 1(1/0/0)
EPHX2 epoxide hydrolase 2 8p21 Mapped by LD-proxy, rSNP target

SNPs in LD with rs60646603 (count: 2)
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: 2)


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