Variant report

Variant	rs11070890
Chromosome Location	chr15:52555025-52555026
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52554935..52557225-chr15:52859729..52862612,2	MCF-7	breast:
2	chr15:52553916..52556418-chr15:52615344..52617187,2	MCF-7	breast:
3	chr15:52552685..52555324-chr15:52573608..52576301,2	MCF-7	breast:
4	chr15:52541572..52560373-chr15:52569752..52591000,64	MCF-7	breast:
5	chr15:52545028..52546786-chr15:52553340..52555593,3	MCF-7	breast:
6	chr15:52536643..52538953-chr15:52552429..52555454,3	MCF-7	breast:
7	chr15:52539435..52542328-chr15:52552750..52555467,4	MCF-7	breast:
8	chr15:52536664..52559220-chr15:52576974..52590204,72	MCF-7	breast:
9	chr15:52553415..52555370-chr15:52556618..52558914,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000128989	Chromatin interaction
ENSG00000197535	Chromatin interaction
ENSG00000128833	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10851510	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10851511	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11070886	0.85[AMR][1000 genomes]
rs17707198	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs4432216	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs4496072	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4514621	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs4774617	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4776031	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4776033	0.93[YRI][hapmap];0.95[AFR][1000 genomes]
rs58479271	1.00[EUR][1000 genomes]
rs59060156	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59211915	0.84[EUR][1000 genomes]
rs60279448	0.84[ASN][1000 genomes]
rs61367038	1.00[EUR][1000 genomes]
rs61551630	0.92[EUR][1000 genomes]
rs61591742	0.83[ASN][1000 genomes]
rs6493548	0.92[AMR][1000 genomes]
rs7165256	0.89[CHB][hapmap];0.84[JPT][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7169177	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7171825	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs7172026	0.94[YRI][hapmap];0.90[AFR][1000 genomes]
rs7172236	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7180204	0.92[AMR][1000 genomes]
rs8025608	0.84[JPT][hapmap]
rs9806461	1.00[EUR][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	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52524400-52579400	Weak transcription	Small Intestine	intestine
2	chr15:52543600-52555400	Weak transcription	Liver	Liver
3	chr15:52547000-52555800	Weak transcription	Fetal Intestine Large	intestine
4	chr15:52549000-52557800	Weak transcription	Fetal Brain Male	brain
5	chr15:52549400-52567200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr15:52549600-52557400	Weak transcription	Thymus	Thymus
7	chr15:52550000-52579200	Weak transcription	Fetal Kidney	kidney
8	chr15:52550200-52572200	Strong transcription	HepG2	liver
9	chr15:52552200-52557200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:52552800-52556000	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr15:52553000-52555400	Enhancers	Primary B cells from peripheral blood	blood
12	chr15:52553000-52556000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:52553000-52556200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr15:52553000-52556400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:52553000-52556400	Enhancers	Primary T cells fromperipheralblood	blood
16	chr15:52553000-52562600	Strong transcription	Fetal Intestine Small	intestine
17	chr15:52553200-52555800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr15:52553200-52555800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr15:52553200-52555800	Enhancers	Adipose Nuclei	Adipose
20	chr15:52553200-52556200	Genic enhancers	Pancreas	Pancrea
21	chr15:52553200-52556600	Enhancers	Fetal Thymus	thymus
22	chr15:52553200-52557000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr15:52553200-52575400	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr15:52553400-52555200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:52553400-52555200	Enhancers	Primary B cells from cord blood	blood
26	chr15:52553400-52555400	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr15:52553400-52555600	Enhancers	H1 Cell Line	embryonic stem cell
28	chr15:52553400-52555600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr15:52553400-52555800	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr15:52553400-52555800	Enhancers	Brain Angular Gyrus	brain
31	chr15:52553400-52555800	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr15:52553400-52556000	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr15:52553400-52556000	Genic enhancers	Gastric	stomach
34	chr15:52553400-52556200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr15:52553400-52556200	Enhancers	HMEC	breast
36	chr15:52553400-52556400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr15:52553400-52557200	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr15:52553600-52555200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr15:52553600-52555200	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr15:52553600-52555200	Enhancers	Brain Anterior Caudate	brain
41	chr15:52553600-52555200	Enhancers	Fetal Heart	heart
42	chr15:52553600-52555200	Genic enhancers	Fetal Stomach	stomach
43	chr15:52553600-52555200	Enhancers	Lung	lung
44	chr15:52553600-52555200	Enhancers	NH-A	brain
45	chr15:52553600-52555400	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr15:52553600-52555400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr15:52553600-52555400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr15:52553600-52555400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr15:52553600-52555400	Enhancers	HUVEC	blood vessel
50	chr15:52553600-52555800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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