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.


rs_ID	Annotation	No. of Association Results(Positive/Negative/Trend)	r²[population]
rs1143633	downstream_gene_variant(ENST00000477398, ENST00000496280); intron_variant(ENST00000487639, ENST00000263341, ENST00000418817, ENST00000491056, ENST00000416750, ENST00000432018); non_coding_transcript_variant(ENST00000487639, ENST00000491056)	1(1/0/0)	0.9879[EUR]

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs3917368	rs1143643 rs1143633	downstream_gene_variant	0.9401[EUR]
rs3181067	rs1143643 rs1143633	downstream_gene_variant	0.9880[EUR]

SNP related eQTL (count: 1)

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