Variant report

Variant	rs12280002
Chromosome Location	chr11:46671393-46671394
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:46636371..46638995-chr11:46670648..46672876,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175224	Chromatin interaction
ENSG00000180423	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11038965	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12273343	0.83[AFR][1000 genomes]
rs58638551	1.00[AMR][1000 genomes]
rs60105423	1.00[AMR][1000 genomes]
rs61752936	1.00[AMR][1000 genomes]
rs7117290	1.00[AMR][1000 genomes]
rs7118357	1.00[AMR][1000 genomes]
rs7930857	1.00[AMR][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	nsv1044225	chr11:46472580-46771102	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv541030	chr11:46472580-46771102	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv897321	chr11:46515902-46673344	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46640800-46673000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr11:46641800-46680800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr11:46642000-46685000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:46643600-46690800	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr11:46652200-46678400	Weak transcription	Fetal Brain Male	brain
6	chr11:46652200-46695600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr11:46654200-46671800	Weak transcription	HMEC	breast
8	chr11:46656600-46691200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr11:46659600-46695200	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr11:46661000-46681000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr11:46661200-46671600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr11:46662400-46676200	Weak transcription	Stomach Mucosa	stomach
13	chr11:46664000-46680400	Strong transcription	Fetal Intestine Large	intestine
14	chr11:46664000-46690600	Strong transcription	Primary T cells from cord blood	blood
15	chr11:46664200-46680600	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr11:46664200-46680600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr11:46664200-46689600	Strong transcription	Dnd41	blood
18	chr11:46664200-46692600	Strong transcription	Duodenum Mucosa	Duodenum
19	chr11:46664200-46695400	Strong transcription	Primary B cells from peripheral blood	blood
20	chr11:46664400-46685400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr11:46664400-46691000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr11:46664400-46691400	Strong transcription	Fetal Thymus	thymus
23	chr11:46664800-46679800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr11:46665200-46675000	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr11:46665400-46675000	Strong transcription	Primary B cells from cord blood	blood
26	chr11:46665600-46680600	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr11:46665600-46691000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr11:46665800-46679200	Strong transcription	Placenta	Placenta
29	chr11:46665800-46685000	Strong transcription	Stomach Smooth Muscle	stomach
30	chr11:46665800-46688600	Strong transcription	Fetal Muscle Leg	muscle
31	chr11:46665800-46690600	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr11:46665800-46695200	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr11:46666000-46681800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr11:46666000-46691000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr11:46666000-46695400	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr11:46666200-46674600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
37	chr11:46666400-46673200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr11:46666400-46682000	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr11:46666800-46674400	Strong transcription	Placenta Amnion	Placenta Amnion
40	chr11:46667000-46690800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr11:46667000-46691000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr11:46667000-46691600	Strong transcription	Thymus	Thymus
43	chr11:46667200-46674600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
44	chr11:46667200-46695400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr11:46667200-46695600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr11:46667200-46717000	Strong transcription	Brain Germinal Matrix	brain
47	chr11:46667400-46686800	Strong transcription	Lung	lung
48	chr11:46667400-46696000	Strong transcription	Fetal Brain Female	brain
49	chr11:46667800-46674200	Weak transcription	NHEK	skin
50	chr11:46668400-46671800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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