Variant report

Variant	rs489275
Chromosome Location	chr11:62567383-62567384
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:62567347-62567501	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr11:62565988-62568522	K562	blood:	n/a	n/a
3	POLR2A	chr11:62565877-62567569	GM12878	blood:	n/a	n/a
4	POLR2A	chr11:62566688-62567542	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:62565367..62576307-chr11:62617328..62626616,39	K562	blood:
2	chr11:62492481..62494967-chr11:62566351..62569330,2	MCF-7	breast:

Variant related genes	Relation type
NXF1	TF binding region
ENSG00000255717	Chromatin interaction
ENSG00000234857	Chromatin interaction
ENSG00000214753	Chromatin interaction
ENSG00000168003	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11822922	1.00[EUR][1000 genomes]
rs12273912	1.00[EUR][1000 genomes]
rs1787724	1.00[EUR][1000 genomes]
rs2510538	1.00[EUR][1000 genomes]
rs2584915	1.00[EUR][1000 genomes]
rs2584917	1.00[EUR][1000 genomes]
rs2730030	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2730033	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2956139	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2958240	1.00[EUR][1000 genomes]
rs481272	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs482331	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs486451	1.00[EUR][1000 genomes]
rs4963309	1.00[EUR][1000 genomes]
rs506132	1.00[EUR][1000 genomes]
rs507101	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs514401	1.00[EUR][1000 genomes]
rs518780	1.00[EUR][1000 genomes]
rs519473	1.00[EUR][1000 genomes]
rs523328	1.00[EUR][1000 genomes]
rs544573	1.00[EUR][1000 genomes]
rs560006	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs560603	1.00[AMR][1000 genomes]
rs560618	1.00[EUR][1000 genomes]
rs561385	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs561520	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56226867	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56262657	1.00[EUR][1000 genomes]
rs564587	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs572513	1.00[EUR][1000 genomes]
rs573146	1.00[EUR][1000 genomes]
rs57338459	1.00[EUR][1000 genomes]
rs575134	1.00[EUR][1000 genomes]
rs577071	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57858466	1.00[EUR][1000 genomes]
rs592337	1.00[EUR][1000 genomes]
rs595108	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60568977	1.00[EUR][1000 genomes]
rs60668695	1.00[EUR][1000 genomes]
rs619109	1.00[EUR][1000 genomes]
rs646194	1.00[EUR][1000 genomes]
rs692773	1.00[EUR][1000 genomes]
rs694678	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73487819	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73487834	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73487878	1.00[EUR][1000 genomes]
rs73487879	1.00[EUR][1000 genomes]
rs73487880	1.00[EUR][1000 genomes]
rs73490026	1.00[EUR][1000 genomes]
rs73502133	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915636	chr11:62016992-62713565	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1441 gene(s)	inside rSNPs	diseases
2	nsv532283	chr11:62201358-62863475	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1433 gene(s)	inside rSNPs	diseases
3	nsv532284	chr11:62220043-62630253	Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1401 gene(s)	inside rSNPs	diseases
4	nsv497903	chr11:62330308-62608042	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	489 gene(s)	inside rSNPs	diseases
5	nsv897623	chr11:62438819-62603916	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	215 gene(s)	inside rSNPs	diseases
6	nsv508636	chr11:62547114-62644458	Transcr. at gene 5' and 3' Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1195 gene(s)	inside rSNPs	diseases
7	nsv1051308	chr11:62564713-62673136	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1199 gene(s)	inside rSNPs	diseases
8	nsv541058	chr11:62564713-62673136	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1199 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62559400-62571200	Genic enhancers	Placenta	Placenta
2	chr11:62559400-62572000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:62559800-62571400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr11:62560000-62570400	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr11:62560000-62571000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr11:62560000-62571200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:62560000-62571400	Strong transcription	H9 Cell Line	embryonic stem cell
8	chr11:62560000-62571400	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr11:62560200-62568800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr11:62560200-62569000	Strong transcription	GM12878-XiMat	blood
11	chr11:62560200-62569800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr11:62560200-62570000	Strong transcription	Right Ventricle	heart
13	chr11:62560200-62570200	Strong transcription	Esophagus	oesophagus
14	chr11:62560200-62570200	Strong transcription	NHDF-Ad	bronchial
15	chr11:62560200-62570400	Strong transcription	Brain Angular Gyrus	brain
16	chr11:62560200-62570400	Strong transcription	Colonic Mucosa	Colon
17	chr11:62560200-62570800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr11:62560200-62570800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr11:62560200-62570800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr11:62560200-62570800	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr11:62560200-62570800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr11:62560200-62570800	Strong transcription	Placenta Amnion	Placenta Amnion
23	chr11:62560200-62570800	Strong transcription	Spleen	Spleen
24	chr11:62560200-62571000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr11:62560200-62571000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr11:62560200-62571000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr11:62560200-62571000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr11:62560200-62571000	Strong transcription	Adipose Nuclei	Adipose
29	chr11:62560200-62571000	Strong transcription	Liver	Liver
30	chr11:62560200-62571000	Strong transcription	Brain Anterior Caudate	brain
31	chr11:62560200-62571000	Strong transcription	Brain Cingulate Gyrus	brain
32	chr11:62560200-62571000	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr11:62560200-62571000	Strong transcription	Brain Substantia Nigra	brain
34	chr11:62560200-62571000	Strong transcription	Fetal Thymus	thymus
35	chr11:62560200-62571000	Strong transcription	Lung	lung
36	chr11:62560200-62571000	Strong transcription	Thymus	Thymus
37	chr11:62560200-62571000	Strong transcription	HUVEC	blood vessel
38	chr11:62560200-62571000	Strong transcription	NH-A	brain
39	chr11:62560200-62571000	Strong transcription	Osteobl	bone
40	chr11:62560200-62571200	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr11:62560200-62571200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr11:62560200-62571200	Strong transcription	Brain Germinal Matrix	brain
43	chr11:62560200-62571200	Strong transcription	Left Ventricle	heart
44	chr11:62560200-62571200	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr11:62560200-62571200	Strong transcription	A549	lung
46	chr11:62560200-62571200	Strong transcription	HSMMtube	muscle
47	chr11:62560200-62571200	Strong transcription	NHEK	skin
48	chr11:62560200-62571400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr11:62560200-62571400	Strong transcription	Fetal Muscle Trunk	muscle
50	chr11:62560400-62569800	Strong transcription	HepG2	liver

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