Variant report

Variant	rs10853094
Chromosome Location	chr17:46176062-46176063
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46175023..46180196-chr17:46181333..46189268,23	MCF-7	breast:
2	chr17:46166805..46169680-chr17:46175249..46176872,2	K562	blood:
3	chr17:46174648..46181471-chr17:46183317..46187457,20	MCF-7	breast:
4	chr17:46168437..46170885-chr17:46173334..46176896,3	MCF-7	breast:
5	chr17:46174713..46176905-chr17:46204166..46206499,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000002919	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1010228	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11079806	0.83[EUR][1000 genomes]
rs11079807	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11079808	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11079809	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11649919	0.85[EUR][1000 genomes]
rs11651097	0.85[EUR][1000 genomes]
rs11655407	0.85[EUR][1000 genomes]
rs11869625	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12450620	0.82[EUR][1000 genomes]
rs12600980	0.87[ASN][1000 genomes]
rs12602948	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12936731	0.82[EUR][1000 genomes]
rs12941295	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12943543	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12949879	0.85[EUR][1000 genomes]
rs12950213	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12950402	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12952163	0.86[EUR][1000 genomes]
rs1860866	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2051821	0.83[EUR][1000 genomes]
rs2109984	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35361214	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35688835	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3744346	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3744347	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3785737	0.83[ASN][1000 genomes]
rs4794441	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4794442	0.96[ASN][1000 genomes]
rs4794443	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4794448	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4794449	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4794450	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4794451	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4794453	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58203448	0.81[EUR][1000 genomes]
rs58595405	0.85[EUR][1000 genomes]
rs58624511	0.86[EUR][1000 genomes]
rs62064953	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6504024	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6504025	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6504031	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6504032	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6847	0.85[EUR][1000 genomes]
rs71369829	0.86[EUR][1000 genomes]
rs7209585	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7209730	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7212202	0.82[EUR][1000 genomes]
rs7213339	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7217496	0.85[EUR][1000 genomes]
rs7218700	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7220520	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7221441	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7222136	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7224014	0.85[EUR][1000 genomes]
rs8065670	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8065993	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8066049	0.86[ASN][1000 genomes]
rs8066391	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8069889	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8071199	0.85[ASN][1000 genomes]
rs8075500	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8076380	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8077860	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8078125	0.85[EUR][1000 genomes]
rs8080662	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs875065	0.82[EUR][1000 genomes]
rs875066	0.82[EUR][1000 genomes]
rs9747001	0.84[EUR][1000 genomes]
rs978263	0.87[ASN][1000 genomes]
rs9807087	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9890691	0.87[ASN][1000 genomes]
rs9899275	0.82[EUR][1000 genomes]
rs9899461	0.82[EUR][1000 genomes]
rs9910516	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv908576	chr17:46147807-46260366	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10853094	SNX11	cis	Whole Blood	GTEx
rs10853094	PNPO	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46144800-46177800	Weak transcription	Right Ventricle	heart
2	chr17:46147800-46177600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr17:46149000-46178000	Weak transcription	Lung	lung
4	chr17:46152400-46177200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr17:46152600-46176800	Weak transcription	K562	blood
6	chr17:46152600-46177000	Weak transcription	HSMMtube	muscle
7	chr17:46153800-46176800	Weak transcription	NHLF	lung
8	chr17:46154200-46176800	Weak transcription	HMEC	breast
9	chr17:46154200-46177600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr17:46154400-46176800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr17:46154400-46177000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr17:46154400-46177200	Weak transcription	Placenta	Placenta
13	chr17:46154400-46177600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr17:46154400-46177600	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr17:46154400-46177600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr17:46154400-46177600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr17:46154400-46177600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr17:46154400-46177600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr17:46154400-46177800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr17:46154600-46176800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr17:46154600-46177000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr17:46154600-46177000	Weak transcription	Osteobl	bone
23	chr17:46154600-46177600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr17:46163400-46177600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr17:46163600-46177200	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr17:46163600-46177600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr17:46163800-46176800	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr17:46163800-46176800	Weak transcription	Brain Angular Gyrus	brain
29	chr17:46163800-46176800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr17:46163800-46177000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr17:46163800-46177200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr17:46163800-46177600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr17:46163800-46177600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr17:46163800-46177600	Weak transcription	Stomach Mucosa	stomach
35	chr17:46163800-46177800	Weak transcription	Pancreas	Pancrea
36	chr17:46164000-46177000	Weak transcription	Fetal Lung	lung
37	chr17:46164000-46177200	Weak transcription	Ovary	ovary
38	chr17:46165800-46177000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr17:46166400-46176800	Weak transcription	HUVEC	blood vessel
40	chr17:46167600-46176800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr17:46167800-46177200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr17:46171000-46177000	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr17:46171200-46177200	Weak transcription	HSMM	muscle
44	chr17:46171400-46177600	Weak transcription	Adipose Nuclei	Adipose
45	chr17:46171400-46177800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr17:46171800-46177200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr17:46171800-46177400	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr17:46171800-46177600	Weak transcription	Primary B cells from peripheral blood	blood
49	chr17:46171800-46177600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr17:46171800-46177600	Weak transcription	Rectal Mucosa Donor 31	rectum

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