SNP Report

Basic Info

Name	rs60646603 dbSNP Ensembl
Location	8:27470188 - 27470188(+)
Variant Seq	G
Ancestral Allele	A
Ref Seq	A
Minor Allele Frequence	0.00499201
Annotation	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant
Variant Effect	downstream_gene_variant(ENST00000520650, ENST00000520208); upstream_gene_variant(ENST00000522008, ENST00000520600); intron_variant(ENST00000518712, ENST00000523695, ENST00000521921, ENST00000407991, ENST00000524096, ENST00000240132, ENST00000520933); NMD_transcript_variant(ENST00000523695)
SIFT Annotation	deleterious
SIFT Variant Effect	deleterious(ENST00000523695, ENST00000520933, ENST00000407991, ENST00000524096)
PolyPhen Annotation	probably_damaging
PolyPhen Variant Effect	probably_damaging(ENST00000523695, ENST00000520933, ENST00000407991, ENST00000524096)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	Chromatin interactive region
Chromatin State	Weak transcription;Enhancers
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
Kimbrel, N. A.,2015	PTSD	In the NHB sample, main effect: P-value=0.03028. In the NHB sample, main effect: P-value=0.03028.	Nominally significant associations (p<.05) were observed, bu...... Nominally significant associations (p<.05) were observed, but it didn't met multiple-testing threshold. More...	Significant

G*E study related association result (count: 1)

Reference	Phenotype	Environment	Statistical Values	Author Comments	Marker's Category
Kimbrel, N. A.,2015	PTSD	Smoking status	GxE interactions among NHB participants: P-value=0.7831. GxE interactions among NHB participants: P-value=0.7831.	No GxE interactions were statistically significant among NHB...... No GxE interactions were statistically significant among NHB participants. More...	Non-significant

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
CHRNA2	cholinergic receptor, nicotinic alpha 2	8p21	1(1/0/0)
EPHX2	epoxide hydrolase 2	8p21	Mapped by LD-proxy, rSNP target

SNPs in LD with rs60646603 (count: 2)

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]
rs60389529	rs60646603	upstream_gene_variant	1.0000[AFR]
rs61310589	rs60646603	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0000[AFR]

SNP related eQTL (count: 1)

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