SNP Report

Basic Info

Name	rs16944 dbSNP Ensembl
Location	2:112837290 - 112837290(+)
Variant Seq	G
Ancestral Allele	A
Ref Seq	A
Minor Allele Frequence	0.490615
Annotation	upstream_gene_variant
Variant Effect	upstream_gene_variant(ENST00000432018, ENST00000491056, ENST00000263341, ENST00000477398, ENST00000416750, ENST00000623243, ENST00000487639, ENST00000418817, ENST00000496280)
SIFT Annotation	tolerated
SIFT Variant Effect	tolerated(ENST00000418817, ENST00000263341)
PolyPhen Annotation	benign
PolyPhen Variant Effect	benign(ENST00000418817, ENST00000263341)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	n/a
Chromatin State	Enhancers;Weak transcription;Flanking Active TSS;Bivalent Enhancer
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	A carriage: OR=0.44, P-value=0.0028, corrected P-value=0.014 A carriage: OR=0.44, P-value=0.0028, corrected P-value=0.014	IL1B rs16944 A minor allele frequency was also significantly...... IL1B rs16944 A minor allele frequency was also significantly lower in patients than in controls. The carriers of this allele were overrepresented in controls compared to patients. More...	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 rs16944 (count: 8)

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	Literature-origin SNPs with LD	Annotation	r²[population]
rs2708916	rs16944	downstream_gene_variant	0.8398[EUR]
rs1143629	rs16944	upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.9886[EUR]
rs6735739	rs16944	upstream_gene_variant	0.9772[EUR]
rs2708914	rs16944	downstream_gene_variant	0.8558[EUR]
rs2466446	rs16944	upstream_gene_variant	0.8774[EUR]
rs10169916	rs16944	downstream_gene_variant	0.9885[EUR]
rs13013349	rs16944	non_coding_transcript_exon_variant; upstream_gene_variant; non_coding_transcript_variant	0.9885[EUR]
rs1143627	rs16944	5_prime_UTR_variant; upstream_gene_variant	0.9943[EUR]

SNP related eQTL (count: 1)

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