Variant report

Variant	rs12577241
Chromosome Location	chr11:9710174-9710175
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9708443..9711288-chr11:9711524..9713112,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11042471	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11042472	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11042473	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11042474	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11042475	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11042477	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11042478	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12272167	0.82[AMR][1000 genomes]
rs12275468	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12291809	0.88[ASN][1000 genomes]
rs12295129	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12576997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1390680	0.82[AMR][1000 genomes]
rs1496477	0.82[AMR][1000 genomes]
rs2088293	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2101902	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2572936	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2572937	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2572938	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2572939	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2572941	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2572947	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2572948	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2572949	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2572952	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2645014	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2645015	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2645016	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2645018	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2645019	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2645021	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2645022	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2645023	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2645024	0.82[AMR][1000 genomes]
rs2649047	0.82[AMR][1000 genomes]
rs34780673	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360044	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs360045	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs360046	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs360048	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs360050	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs360052	0.96[ASN][1000 genomes]
rs360053	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs416766	0.82[AMR][1000 genomes]
rs57239484	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67598578	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73408298	0.84[EUR][1000 genomes]
rs73408300	0.88[EUR][1000 genomes]
rs73410140	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs920081	0.82[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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv553468	chr11:9667828-9827871	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9686600-9711200	Weak transcription	Esophagus	oesophagus
2	chr11:9686800-9710800	Weak transcription	Aorta	Aorta
3	chr11:9686800-9716400	Weak transcription	Ovary	ovary
4	chr11:9687200-9710200	Weak transcription	Hela-S3	cervix
5	chr11:9687400-9710800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr11:9701000-9712800	Weak transcription	Small Intestine	intestine
7	chr11:9702800-9711000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr11:9702800-9711200	Weak transcription	Lung	lung
9	chr11:9703200-9710800	Weak transcription	Fetal Muscle Leg	muscle
10	chr11:9703400-9710800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr11:9703600-9711000	Weak transcription	Fetal Intestine Large	intestine
12	chr11:9703800-9710200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr11:9703800-9710800	Genic enhancers	Primary B cells from peripheral blood	blood
14	chr11:9703800-9714400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr11:9704200-9723600	Weak transcription	HepG2	liver
16	chr11:9705000-9711200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr11:9705200-9710600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr11:9705600-9711200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr11:9706800-9710200	Weak transcription	Fetal Intestine Small	intestine
20	chr11:9708200-9711200	Weak transcription	Pancreas	Pancrea
21	chr11:9708400-9711800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr11:9708400-9712000	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr11:9708600-9711000	Weak transcription	Placenta	Placenta
24	chr11:9708800-9710200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:9708800-9710600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr11:9708800-9711600	Enhancers	Fetal Heart	heart
27	chr11:9709000-9710200	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr11:9709000-9710600	Enhancers	Brain Substantia Nigra	brain
29	chr11:9709000-9712200	Enhancers	Adipose Nuclei	Adipose
30	chr11:9709200-9710200	Enhancers	NHEK	skin
31	chr11:9709200-9710600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr11:9709200-9710600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr11:9709200-9710600	Enhancers	Brain Anterior Caudate	brain
34	chr11:9709200-9710600	Enhancers	Brain Hippocampus Middle	brain
35	chr11:9709200-9710600	Enhancers	HMEC	breast
36	chr11:9709200-9710600	Enhancers	Osteobl	bone
37	chr11:9709200-9710800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr11:9709200-9710800	Enhancers	Brain Cingulate Gyrus	brain
39	chr11:9709200-9711600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr11:9709200-9711600	Enhancers	Rectal Smooth Muscle	rectum
41	chr11:9709200-9711800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr11:9709200-9711800	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr11:9709200-9711800	Enhancers	Muscle Satellite Cultured Cells	--
44	chr11:9709200-9711800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr11:9709400-9710200	Enhancers	Brain Angular Gyrus	brain
46	chr11:9709400-9710200	Enhancers	Psoas Muscle	Psoas
47	chr11:9709400-9710200	Enhancers	NH-A	brain
48	chr11:9709400-9710600	Enhancers	Primary hematopoietic stem cells	blood
49	chr11:9709400-9710600	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr11:9709400-9710600	Enhancers	Right Ventricle	heart

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