SNP Report

Basic Info

Name	rs11599164 dbSNP Ensembl
Location	10:60072226 - 60072226(+)
Variant Seq	T
Ancestral Allele	G
Ref Seq	G
Minor Allele Frequence	0.0313498
Annotation	missense_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant
Variant Effect	missense_variant(ENST00000621739, ENST00000280772); upstream_gene_variant(ENST00000613207, ENST00000610901); intron_variant(ENST00000511043, ENST00000373820, ENST00000503366, ENST00000616444, ENST00000355288, ENST00000373827, ENST00000618374, ENST00000610321); NMD_transcript_variant(ENST00000621739)
SIFT Annotation	deleterious_-_low_confidence
SIFT Variant Effect	deleterious_-_low_confidence(ENST00000621739, ENST00000280772)
PolyPhen Annotation	benign
PolyPhen Variant Effect	benign(ENST00000621739, ENST00000280772)
rSNP?	Yes Link in rVarBase
Related Regulatory Elements	n/a
Chromatin State	Weak transcription;Strong transcription
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
Logue, M. W.,2013	PTSD	OR=0.48, P-value=0.00060, corrected P-value=0.045 OR=0.48, P-value=0.00060, corrected P-value=0.045	The SNP was associated with PTSD at the P-value<0.01 level. The SNP was associated with PTSD at the P-value<0.01 level.	Significant

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Association Results (Positive/Negative/Trend)
ANK3	ankyrin 3, node of Ranvier (ankyrin G)	10q21	2(2/0/0)

SNPs in LD with rs11599164 (count: 14)

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: 3)

rs_ID	Annotation	No. of Association Results(Positive/Negative/Trend)	r²[population]

rs7917800	downstream_gene_variant(ENST00000508449, ENST00000622427); upstream_gene_variant(ENST00000365320); intron_variant(ENST00000503366, ENST00000610321, ENST00000511043, ENST00000280772, ENST00000373820, ENST00000373827, ENST00000618374, ENST00000355288, ENST00000616444)	1(1/0/0)	0.8530[EUR]
rs17208576	synonymous_variant(ENST00000610321, ENST00000280772); upstream_gene_variant(ENST00000613207, ENST00000610901, ENST00000621739); intron_variant(ENST00000373827, ENST00000618374, ENST00000616444, ENST00000511043, ENST00000373820, ENST00000355288, ENST00000503366)	1(1/0/0)	1.0000[EUR]
rs28932171	missense_variant(ENST00000621739, ENST00000280772); upstream_gene_variant(ENST00000610901, ENST00000613207); intron_variant(ENST00000610321, ENST00000616444, ENST00000511043, ENST00000503366, ENST00000618374, ENST00000373827, ENST00000373820, ENST00000355288); NMD_transcript_variant(ENST00000621739)	1(1/0/0)	1.0000[EUR]

LD-proxies (count: 11)

rs_ID	Literature-origin SNPs with LD	Annotation	r²[population]
rs72818480	rs28932171 rs7917800 rs17208576 rs11599164	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant	0.9318[EUR]
rs17802184	rs28932171 rs7917800 rs17208576 rs11599164	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant	0.9318[EUR]
rs11593500	rs7098848 rs28932171 rs7917800 rs17208576 rs11599164	downstream_gene_variant; upstream_gene_variant; intron_variant	0.9862[EUR]
rs17802232	rs28932171 rs7917800 rs17208576 rs11599164	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant	0.9583[EUR]
rs2393610	rs28932171 rs7917800 rs17208576 rs11599164	downstream_gene_variant; upstream_gene_variant; intron_variant	0.9449[EUR]
rs17208611	rs7098848 rs28932171 rs7917800 rs17208576 rs11599164	downstream_gene_variant; upstream_gene_variant; intron_variant	0.9862[EUR]
rs11593609	rs7098848 rs28932171 rs7917800 rs17208576 rs11599164	downstream_gene_variant; upstream_gene_variant; intron_variant	0.9862[EUR]
rs17802208	rs28932171 rs7917800 rs17208576 rs11599164	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant	0.9318[EUR]
rs4480489	rs28932171 rs17208576 rs11599164	downstream_gene_variant; upstream_gene_variant; intron_variant; NMD_transcript_variant	0.8374[EUR]
rs72818490	rs7098848 rs28932171 rs7917800 rs17208576 rs11599164	downstream_gene_variant; upstream_gene_variant; intron_variant	0.8024[EUR]
rs17207897	rs28932171 rs7917800 rs17208576 rs11599164	downstream_gene_variant; upstream_gene_variant; intron_variant; non_coding_transcript_variant	0.9449[EUR]

SNP related eQTL (count: 1)

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