Variant report

Variant	rs10896643
Chromosome Location	chr11:57551554-57551555
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	chr11:57545406..57547871-chr11:57550321..57552770,3	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10444364	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10736687	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10750868	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12284427	0.87[AMR][1000 genomes]
rs1313360	1.00[ASN][1000 genomes]
rs1553827	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1798174	1.00[ASN][1000 genomes]
rs1939322	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2441951	1.00[ASN][1000 genomes]
rs2860261	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34430954	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs474073	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs474464	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs505995	1.00[ASN][1000 genomes]
rs523739	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs542777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs552122	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs554140	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs557051	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55786036	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55838210	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56879142	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57201273	1.00[ASN][1000 genomes]
rs57260887	1.00[ASN][1000 genomes]
rs57759830	1.00[ASN][1000 genomes]
rs58176671	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs585190	1.00[ASN][1000 genomes]
rs58851976	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59046396	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60076210	1.00[ASN][1000 genomes]
rs60282001	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60897155	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61444907	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61638601	1.00[ASN][1000 genomes]
rs61743110	1.00[ASN][1000 genomes]
rs627861	1.00[ASN][1000 genomes]
rs635663	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs637116	1.00[ASN][1000 genomes]
rs648412	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7103407	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7103768	1.00[ASN][1000 genomes]
rs7105331	1.00[ASN][1000 genomes]
rs7110490	1.00[ASN][1000 genomes]
rs7112557	1.00[ASN][1000 genomes]
rs7118249	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7118308	1.00[ASN][1000 genomes]
rs7122105	1.00[AMR][1000 genomes]
rs7131175	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73472468	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73474417	1.00[ASN][1000 genomes]
rs73474449	1.00[ASN][1000 genomes]
rs73474453	1.00[ASN][1000 genomes]
rs73474454	1.00[ASN][1000 genomes]
rs73474455	1.00[ASN][1000 genomes]
rs73474476	1.00[ASN][1000 genomes]
rs73482748	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73482786	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73482796	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73482801	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7928666	1.00[ASN][1000 genomes]
rs7938752	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs947940	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers 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 miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv508633	chr11:57419585-57560045	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers 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 target site	58 gene(s)	inside rSNPs	diseases
7	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57539600-57552000	Enhancers	Placenta	Placenta
2	chr11:57545200-57551600	Weak transcription	Gastric	stomach
3	chr11:57545200-57555400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:57546400-57559000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr11:57546400-57559200	Enhancers	Stomach Mucosa	stomach
6	chr11:57546600-57554000	Genic enhancers	Fetal Intestine Small	intestine
7	chr11:57546800-57554800	Weak transcription	Fetal Brain Female	brain
8	chr11:57546800-57564000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr11:57547000-57555400	Enhancers	Duodenum Mucosa	Duodenum
10	chr11:57547000-57558600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr11:57547000-57558600	Enhancers	Liver	Liver
12	chr11:57547200-57552000	Enhancers	Brain Angular Gyrus	brain
13	chr11:57547200-57552400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr11:57547200-57552800	Weak transcription	Dnd41	blood
15	chr11:57547200-57555200	Weak transcription	Fetal Brain Male	brain
16	chr11:57547200-57555800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr11:57547400-57554000	Weak transcription	Osteobl	bone
18	chr11:57547400-57555000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:57547400-57555000	Weak transcription	Brain Germinal Matrix	brain
20	chr11:57547400-57558600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr11:57547400-57558800	Weak transcription	Aorta	Aorta
22	chr11:57547800-57554200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr11:57547800-57558600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr11:57548000-57554200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr11:57548400-57554000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr11:57548400-57554400	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr11:57549000-57555000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr11:57549200-57557200	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr11:57549400-57553800	Weak transcription	Fetal Stomach	stomach
30	chr11:57549400-57554000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr11:57549400-57554200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr11:57549400-57554400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr11:57549400-57554400	Weak transcription	NHLF	lung
34	chr11:57549400-57555000	Weak transcription	Spleen	Spleen
35	chr11:57549400-57555800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr11:57549400-57558400	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr11:57549400-57559600	Weak transcription	Hela-S3	cervix
38	chr11:57549600-57552000	Weak transcription	Primary B cells from cord blood	blood
39	chr11:57549600-57552400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr11:57549600-57554200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr11:57549600-57554400	Weak transcription	HSMM	muscle
42	chr11:57549800-57553400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr11:57550000-57554200	Enhancers	Small Intestine	intestine
44	chr11:57550000-57555000	Weak transcription	Fetal Thymus	thymus
45	chr11:57550000-57555800	Weak transcription	HUVEC	blood vessel
46	chr11:57550200-57552400	Enhancers	Psoas Muscle	Psoas
47	chr11:57550200-57553400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr11:57550200-57553800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr11:57550200-57554000	Weak transcription	Brain Anterior Caudate	brain
50	chr11:57550200-57554200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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