SNP Report

Basic Info

Name	rs7208505 dbSNP Ensembl
Location	17:59110368 - 59110368(+)
Variant Seq	A
Ancestral Allele	A
Ref Seq	G
Minor Allele Frequence	0.408347
Annotation	downstream_gene_variant; upstream_gene_variant; 3_prime_UTR_variant; intron_variant; non_coding_transcript_variant
Variant Effect	downstream_gene_variant(ENST00000583976, ENST00000578519, ENST00000437036, ENST00000583927, ENST00000578105, ENST00000580541, ENST00000581068, ENST00000583380); upstream_gene_variant(ENST00000393066, ENST00000583387, ENST00000580122, ENST00000584889, ENST00000625984, ENST00000262294, ENST00000580973, ENST00000393065, ENST00000580620, ENST00000577554); 3_prime_UTR_variant(ENST00000330137); intron_variant(ENST00000451775); non_coding_transcript_variant(ENST00000451775)
SIFT Annotation	tolerated
SIFT Variant Effect	tolerated(ENST00000578105, ENST00000583380, ENST00000330137)
PolyPhen Annotation	possibly_damaging
PolyPhen Variant Effect	possibly_damaging(ENST00000578105, ENST00000583380, ENST00000330137)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	CpG island;Chromatin interactive region
Chromatin State	Weak transcription;Strong transcription;Enhancers
No. of Marker's Association Results	2 (Positive: 0; Negative: 2; 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
Sadeh, N.,2016	PTSD diagnosis	Wald X²<0.99,P-value>0.32 Wald X²<0.99,P-value>0.32	SKA2 genotype was also not a significant predictor of PTSD d...... SKA2 genotype was also not a significant predictor of PTSD diagnosis. More...	Non-significant
Sadeh, N.,2016	PTSD symptoms	B<0.05,P-value>0.66 B<0.05,P-value>0.66	SKA2 genotype was also not a significant predictor of PTSD s...... SKA2 genotype was also not a significant predictor of PTSD symptoms. More...	Non-significant

SNP related genes (count: 4)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
TRIM37	tripartite motif containing 37	17q22	Mapped by Literature SNP, Mapped by LD-proxy, rSNP target
TUBD1	tubulin delta 1	17q23.1	rSNP target
SKA2	spindle and kinetochore associated complex subunit 2	17q23.2	2(0/2/0)
VMP1	vacuole membrane protein 1	17q23.1	rSNP target

SNPs in LD with rs7208505 (count: 25)

The LD data used here is based on 1000 Genome Phase I. LD SNP pairs were selected with a threshold r²<=0.8.

Literature-origin SNPs (count: 0)

LD-proxies (count: 25)

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs58092632	rs7208505	intron_variant; NMD_transcript_variant	0.8039[EUR]
rs12603238	rs7208505	intron_variant; NMD_transcript_variant	0.8398[EUR]
rs8182277	rs7208505	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8552[EUR]
rs8072712	rs7208505	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant	0.8974[EUR]
rs6416933	rs7208505	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8552[EUR]
rs8067264	rs7208505	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9189[EUR]
rs6503896	rs7208505	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9834[EUR]
rs11868348	rs7208505	upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9189[EUR]
rs7503190	rs7208505	downstream_gene_variant; non_coding_transcript_exon_variant; 5_prime_UTR_variant; upstream_gene_variant; non_coding_transcript_variant	0.9189[EUR]
rs8082544	rs7208505	downstream_gene_variant; upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.9189[EUR]
rs4932693	rs7208505	intron_variant; NMD_transcript_variant	0.8039[EUR]
rs7502208	rs7208505	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.8974[EUR]
rs11654986	rs7208505	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9780[EUR]
rs6503893	rs7208505	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8552[EUR]
rs56360354	rs7208505	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0000[EUR]
rs11658974	rs7208505	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9246[EUR]
rs6503894	rs7208505	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8974[EUR]
rs6416932	rs7208505	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.8501[EUR]
rs7214098	rs7208505	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0000[EUR]
rs12051897	rs7208505	upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.9020[EUR]
rs1871751	rs7208505	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0000[EUR]
rs8069033	rs7208505	intron_variant; NMD_transcript_variant	0.8247[EUR]
rs1967415	rs7208505	intron_variant; NMD_transcript_variant	0.8039[EUR]
rs11658694	rs7208505	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0000[EUR]
rs2333410	rs7208505	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.8398[EUR]

SNP related eQTL (count: 1)

Gene Symbol	Gene Existed in PTSDgene?	Tissue	Trans/Cis	Source
CRHR1	Yes	Adipose Subcutaneous	cis	GTEx