SNP Report

Basic Info

Name	rs10170218 dbSNP Ensembl
Location	2:187949717 - 187949717(+)
Variant Seq	C
Ancestral Allele	A
Ref Seq	A
Minor Allele Frequence	0.276158
Annotation	intron_variant; non_coding_transcript_variant
Variant Effect	intron_variant(ENST00000434418); non_coding_transcript_variant(ENST00000434418)
SIFT Annotation	tolerated
SIFT Variant Effect	tolerated(ENST00000339091, ENST00000421427, ENST00000392365, ENST00000409676, ENST00000437725, ENST00000420747, ENST00000233156, ENST00000453013, ENST00000426055, ENST00000417013, ENST00000435414)
PolyPhen Annotation	benign; possibly_damaging
PolyPhen Variant Effect	benign(ENST00000421427, ENST00000392365, ENST00000437725, ENST00000420747, ENST00000233156, ENST00000453013, ENST00000426055, ENST00000417013, ENST00000435414); possibly_damaging(ENST00000339091, ENST00000409676)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	n/a
Chromatin State	Weak transcription
No. of Marker's Association Results	2 (Positive: 1; Negative: 1; Trend: 0)
Source	Literature

SNP related association results

Normal genetic study related association results (count: 2)

Reference	Phenotype	Statistical Values	Author Comments	Marker's Category
Ashley-Koch, A. E.,2015	Current PTSD	In NHB P-value=0.35, in NHW P-value=0.75, meta-analysis P-va...... In NHB P-value=0.35, in NHW P-value=0.75, meta-analysis P-value=0.53. More...	We didn't find significant evidence for this specific SNP in...... We didn't find significant evidence for this specific SNP in our study. More...	Non-significant
Guffanti, G.,2013	PTSD	In the DNHS subjects: B=5.45, P-value=5.10E-08, OR=2.89, 95...... In the DNHS subjects: B=5.45, P-value=5.10E-08, OR=2.89, 95%CI=1.97-4.23.The Bonferroni corrected P-value=0.035. In NHS-II sample: additive genetic model P-value=0.07, genotypic model P-value=0.03, dominant model P-value=0.01. More...	The strongest signal was at SNP rs10170218 with a genome-wid...... The strongest signal was at SNP rs10170218 with a genome-wide significant p-value. And they found suggestive evidence of replication in NHSII. More...	Significant

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
LINC01090	long intergenic non-protein coding RNA 1090	2q32.1	2(1/1/0)

SNPs in LD with rs10170218 (count: 4)

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]
rs12104454	rs10170218	intron_variant; non_coding_transcript_variant	0.9934[EUR]; 1.0000[AFR]; 0.9842[AMR]
rs10221619	rs10170218	intron_variant; non_coding_transcript_variant	1.0000[EUR]; 1.0000[AFR]; 0.9842[AMR]
rs57266241	rs10170218	intron_variant; non_coding_transcript_variant	0.9868[EUR]; 1.0000[AFR]; 0.9682[AMR]
rs12105426	rs10170218	intron_variant; non_coding_transcript_variant	1.0000[EUR]; 0.9707[AFR]; 0.9842[AMR]

SNP related eQTL (count: 1)

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