SNP Report

Basic Info

Name	rs3859123 dbSNP Ensembl
Location	16:9977038 - 9977038(+)
Variant Seq	G
Ancestral Allele	G
Ref Seq	A
Minor Allele Frequence	0.383586
Annotation	intron_variant; non_coding_transcript_variant
Variant Effect	intron_variant(ENST00000562109, ENST00000396573, ENST00000330684, ENST00000566670, ENST00000566683, ENST00000568247); non_coding_transcript_variant(ENST00000566670, ENST00000566683, ENST00000568247)
SIFT Annotation	tolerated
SIFT Variant Effect	tolerated(ENST00000396573, ENST00000330684, ENST00000396575, ENST00000562109, ENST00000535259)
PolyPhen Annotation	benign; probably_damaging
PolyPhen Variant Effect	benign(ENST00000396573, ENST00000330684, ENST00000562109, ENST00000535259); probably_damaging(ENST00000396575)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	n/a
Chromatin State	Weak transcription;Enhancers
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
Nelson, E. C.,2014	PTSD	P-value=0.014, OR=1.20 P-value=0.014, OR=1.20	Although the association of this SNP is of considerably lowe...... Although the association of this SNP is of considerably lower magnitude, it is interesting to note. More...	Non-significant

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
GRIN2A	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	16p13.2	1(0/1/0)

SNPs in LD with rs3859123 (count: 1)

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]
rs3105689	rs3859123	upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.8236[EUR]

SNP related eQTL (count: 1)

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