Variant report

Variant	rs1203552
Chromosome Location	chr11:66012888-66012889
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:66010596..66013412-chr11:66022956..66027010,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174996	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1151532	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1190945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1190946	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1191715	0.88[AFR][1000 genomes]
rs1203551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1203749	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1203750	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1203801	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1300706	0.81[AFR][1000 genomes]
rs1630638	0.88[AFR][1000 genomes]
rs1783562	0.85[AFR][1000 genomes]
rs2430981	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2452687	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3016315	0.92[AFR][1000 genomes]
rs3017606	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs471709	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs472853	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs475817	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs477001	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs485547	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4930332	0.89[AFR][1000 genomes]
rs502898	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs504456	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs505412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs505642	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs510398	0.92[AFR][1000 genomes]
rs512316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs515778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs519911	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs527279	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs541954	1.00[AMR][1000 genomes]
rs547282	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs547892	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs549228	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs551652	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs555527	1.00[AMR][1000 genomes]
rs555826	0.92[AFR][1000 genomes]
rs559298	0.83[AFR][1000 genomes]
rs560105	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs561199	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs561869	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs567414	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs568423	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs571368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs572697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs577301	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs581247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6591196	0.85[AFR][1000 genomes]
rs693382	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7934588	0.82[AFR][1000 genomes]
rs7947668	0.88[AFR][1000 genomes]
rs948358	0.86[AFR][1000 genomes]
rs948477	0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	esv3392427	chr11:65981489-66273695	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
4	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65977600-66018600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr11:65984600-66024200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:65985800-66017800	Weak transcription	Fetal Heart	heart
4	chr11:65989600-66024200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:65990200-66019800	Strong transcription	Primary T cells from cord blood	blood
6	chr11:65990600-66015800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr11:65990600-66018400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr11:65990800-66018600	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr11:65991000-66015400	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr11:65991200-66018600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr11:65991200-66018600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr11:65991600-66018400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr11:65991600-66018400	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr11:65991800-66018400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr11:65993800-66018400	Strong transcription	Stomach Smooth Muscle	stomach
16	chr11:65994400-66015200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr11:65994400-66018600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr11:65994600-66013200	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr11:65994600-66013800	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr11:65994600-66018600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr11:65995000-66018000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr11:65995000-66018800	Strong transcription	Fetal Intestine Small	intestine
23	chr11:65995200-66015600	Strong transcription	Lung	lung
24	chr11:65996000-66024400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr11:65997400-66013800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr11:65997400-66018600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr11:65997600-66013600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr11:65997600-66013800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr11:65997600-66015400	Strong transcription	Brain Germinal Matrix	brain
30	chr11:65997600-66018400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr11:65998000-66013800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr11:65998000-66018600	Strong transcription	Fetal Brain Female	brain
33	chr11:65999800-66013800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr11:65999800-66024000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr11:66000800-66024200	Weak transcription	HMEC	breast
36	chr11:66001600-66024200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr11:66002000-66021000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr11:66003400-66017400	Weak transcription	Hela-S3	cervix
39	chr11:66003400-66024200	Weak transcription	HepG2	liver
40	chr11:66003400-66024200	Weak transcription	NHDF-Ad	bronchial
41	chr11:66004000-66020800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr11:66005000-66014000	Strong transcription	Pancreas	Pancrea
43	chr11:66005200-66013000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
44	chr11:66006000-66015000	Strong transcription	Gastric	stomach
45	chr11:66006800-66017800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr11:66006800-66024600	Weak transcription	Ovary	ovary
47	chr11:66007000-66024200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr11:66007200-66024200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr11:66007800-66024200	Weak transcription	Small Intestine	intestine
50	chr11:66008000-66023800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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