SNP Report

Basic Info

Name	rs6650088 dbSNP Ensembl
Location	1:194347004 - 194347004(+)
Variant Seq	G
Ancestral Allele	A
Ref Seq	A
Minor Allele Frequence	0.126597
Annotation	upstream_gene_variant
Variant Effect	upstream_gene_variant(ENST00000435554)
SIFT Annotation	tolerated
SIFT Variant Effect	tolerated(LRG_507t1, ENST00000367435)
PolyPhen Annotation	possibly_damaging
PolyPhen Variant Effect	possibly_damaging(LRG_507t1, ENST00000367435)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	Chromatin interactive region
Chromatin State	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
Solovieff, N.,2014	PTSD diagnosis	P-value=0.079 P-value=0.079	Achieved nominal levels of significance with PTSD diagnosis,...... Achieved nominal levels of significance with PTSD diagnosis, although was not significant after correction for multiple testing More...	Non-significant

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
RGS2	regulator of G-protein signaling 2	1q31	7(2/5/0)

SNPs in LD with rs6650088 (count: 19)

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]
rs7523366	rs6650088	intron_variant; non_coding_transcript_variant	0.8594[EUR]
rs28835351	rs6650088	upstream_gene_variant	0.8594[EUR]
rs7552792	rs6650088	downstream_gene_variant	0.8108[EUR]
rs6686534	rs6650088	intron_variant; non_coding_transcript_variant	0.8192[EUR]
rs7515996	rs6650088	downstream_gene_variant	0.8192[EUR]
rs12092600	rs6650088	downstream_gene_variant	1.0000[EUR]
rs7554808	rs6650088	upstream_gene_variant	0.8192[EUR]
rs10921541	rs6650088	downstream_gene_variant	0.8594[EUR]
rs12065174	rs6650088	downstream_gene_variant	0.8594[EUR]
rs4345789	rs6650088	intron_variant; non_coding_transcript_variant	0.8192[EUR]
rs7517770	rs6650088	downstream_gene_variant	0.8192[EUR]
rs12083179	rs6650088	intron_variant; non_coding_transcript_variant	0.8249[EUR]
rs10921542	rs6650088	downstream_gene_variant	0.8594[EUR]
rs6671783	rs6650088	intron_variant; non_coding_transcript_variant	0.8192[EUR]
rs7524864	rs6650088	intron_variant; non_coding_transcript_variant	0.8594[EUR]
rs6683050	rs6650088	upstream_gene_variant	0.8192[EUR]
rs10801296	rs6650088	intron_variant; non_coding_transcript_variant	0.8192[EUR]
rs6428220	rs6650088	non_coding_transcript_exon_variant; non_coding_transcript_variant	0.8192[EUR]
rs10921544	rs6650088	downstream_gene_variant	0.8594[EUR]

SNP related eQTL (count: 1)

Gene Symbol	Gene Existed in PTSDgene?	Tissue	Trans/Cis	Source
RP11-259G18.3	No	Adipose Subcutaneous	cis	GTEx