SNP Report

Basic Info

Name	rs8024133 dbSNP Ensembl
Location	15:60838440 - 60838440(+)
Variant Seq	T
Ancestral Allele	C
Ref Seq	C
Minor Allele Frequence	0.373602
Annotation	intron_variant; NMD_transcript_variant; non_coding_transcript_variant
Variant Effect	intron_variant(ENST00000559145, ENST00000335670, ENST00000557822, ENST00000551975, ENST00000561093); NMD_transcript_variant(ENST00000551975); non_coding_transcript_variant(ENST00000559145, ENST00000557822, ENST00000561093)
SIFT Annotation	deleterious_-_low_confidence; tolerated
SIFT Variant Effect	deleterious_-_low_confidence(ENST00000551975); tolerated(ENST00000335670)
PolyPhen Annotation	benign; possibly_damaging
PolyPhen Variant Effect	benign(ENST00000335670); possibly_damaging(ENST00000551975)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	n/a
Chromatin State	Weak transcription;Enhancers;Flanking Active TSS
No. of Marker's Association Results	1 (Positive: 0; Negative: 0; Trend: 1)
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	In discovery group (allele): OR=1.9, P-value=8.8E-07. In discovery group (allele): OR=1.9, P-value=8.8E-07.	It reached the suggestive level of significance in discovery...... It reached the suggestive level of significance in discovery group. More...	Trend

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
RORA	RAR related orphan receptor A	15q21-q22	6(4/2/0)

SNPs in LD with rs8024133 (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	Annotation	No. of Association Results(Positive/Negative/Trend)	r²[population]
rs11071561	intron_variant(ENST00000557822, ENST00000551975, ENST00000335670, ENST00000559145, ENST00000561093); NMD_transcript_variant(ENST00000551975); non_coding_transcript_variant(ENST00000557822, ENST00000559145, ENST00000561093)	1(0/0/1)	0.8877[EUR]; 0.8078[AMR]

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs3959689	rs8024133 rs11071561	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9840[EUR]; 0.9342[AMR]
rs8023252	rs8024133 rs4775301	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8463[EUR]; 0.8192[AMR]

SNP related eQTL (count: 1)

Gene Symbol	Gene Existed in PTSDgene?	Tissue	Trans/Cis	Source
RP11-259G18.3	No	Adipose Subcutaneous	cis	GTEx