SNP Report

Basic Info

Name	rs1143633 dbSNP Ensembl
Location	2:112832890 - 112832890(+)
Variant Seq	T
Ancestral Allele	C
Ref Seq	C
Minor Allele Frequence	0.310903
Annotation	downstream_gene_variant; intron_variant; non_coding_transcript_variant
Variant Effect	downstream_gene_variant(ENST00000477398, ENST00000496280); intron_variant(ENST00000487639, ENST00000263341, ENST00000418817, ENST00000491056, ENST00000416750, ENST00000432018); non_coding_transcript_variant(ENST00000487639, ENST00000491056)
SIFT Annotation	deleterious
SIFT Variant Effect	deleterious(ENST00000418817, ENST00000263341, ENST00000416750, ENST00000432018)
PolyPhen Annotation	benign
PolyPhen Variant Effect	benign(ENST00000418817, ENST00000263341, ENST00000416750, ENST00000432018)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	Chromatin interactive region
Chromatin State	Weak transcription;Genic enhancers;Transcr. at gene 5' nd 3';Enhancers;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
Hovhannisyan, L.,2017	PTSD diagnosis	C carriage: OR=0.40, P-value=0.0002, corrected P-value=0.001 C carriage: OR=0.40, P-value=0.0002, corrected P-value=0.001	IL1B rs1143633 C minor allele frequency was significantly lo...... IL1B rs1143633 C minor allele frequency was significantly lower in PTSD patients than in controls. The carriers of this allele were underrepresented in patients compared to controls. More...	Significant

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
IL1A	interleukin 1 alpha	2q14	rSNP target
IL1B	interleukin 1 beta	2q14	1(1/0/0)

SNPs in LD with rs1143633 (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]
rs1143643	downstream_gene_variant(ENST00000432018, ENST00000416750, ENST00000418817, ENST00000477398, ENST00000496280, ENST00000487639); intron_variant(ENST00000263341, ENST00000491056); non_coding_transcript_variant(ENST00000491056)	1(0/1/0)	0.9879[EUR]

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs3917368	rs1143643 rs1143633	downstream_gene_variant	0.9282[EUR]
rs3181067	rs1143643 rs1143633	downstream_gene_variant	0.9760[EUR]

SNP related eQTL (count: 1)

Gene Symbol	Gene Existed in PTSDgene?	Tissue	Trans/Cis	Source
RP11-707O23.5	No	Adipose Subcutaneous	cis	GTEx