Variant report

Variant	rs1880274
Chromosome Location	chr6:25175151-25175152
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	chr6:25173529..25176944-chr6:25190264..25194655,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222373	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10498722	1.00[JPT][hapmap]
rs11965121	1.00[JPT][hapmap]
rs16890188	1.00[EUR][1000 genomes]
rs2328869	1.00[JPT][hapmap]
rs2394370	1.00[EUR][1000 genomes]
rs2744253	1.00[JPT][hapmap]
rs56145792	1.00[EUR][1000 genomes]
rs6456649	1.00[EUR][1000 genomes]
rs6456650	1.00[EUR][1000 genomes]
rs6456661	1.00[JPT][hapmap]
rs6941305	1.00[EUR][1000 genomes]
rs73729776	1.00[EUR][1000 genomes]
rs73729778	1.00[EUR][1000 genomes]
rs7753443	1.00[EUR][1000 genomes]
rs9461105	1.00[EUR][1000 genomes]
rs9461110	1.00[EUR][1000 genomes]
rs9467436	0.81[ASW][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9467437	0.83[AFR][1000 genomes];1.00[EUR][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	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv1020774	chr6:25154152-25285679	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv538161	chr6:25154152-25285679	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv462663	chr6:25156197-25234884	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv601167	chr6:25156197-25234884	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25165600-25177000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr6:25167000-25177400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:25167600-25175400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:25168800-25177000	Enhancers	Placenta	Placenta
5	chr6:25169000-25177000	Enhancers	Placenta Amnion	Placenta Amnion
6	chr6:25169200-25177400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:25170000-25177400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:25170400-25177000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:25171400-25177000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:25171400-25177200	Enhancers	HMEC	breast
11	chr6:25171600-25180000	Enhancers	Hela-S3	cervix
12	chr6:25172600-25175600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:25172600-25175800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:25172600-25176200	Enhancers	NH-A	brain
15	chr6:25172600-25176400	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr6:25172800-25176400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:25173000-25177000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr6:25173000-25177200	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr6:25173000-25177400	Enhancers	Osteobl	bone
20	chr6:25173000-25178600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:25173200-25175600	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr6:25173200-25176000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:25173200-25176000	Enhancers	A549	lung
24	chr6:25173200-25176200	Enhancers	Esophagus	oesophagus
25	chr6:25173200-25176200	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr6:25173200-25176200	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr6:25173200-25176400	Enhancers	Fetal Intestine Large	intestine
28	chr6:25173200-25176400	Enhancers	Fetal Intestine Small	intestine
29	chr6:25173200-25176400	Enhancers	HSMM	muscle
30	chr6:25173200-25177000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:25173200-25177000	Enhancers	HUVEC	blood vessel
32	chr6:25173200-25177200	Enhancers	Primary hematopoietic stem cells	blood
33	chr6:25173400-25175800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:25173400-25177000	Enhancers	NHEK	skin
35	chr6:25173600-25175600	Weak transcription	Ovary	ovary
36	chr6:25173600-25176200	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr6:25173800-25175600	Enhancers	Stomach Mucosa	stomach
38	chr6:25173800-25177200	Enhancers	HSMMtube	muscle
39	chr6:25174000-25175400	Enhancers	Rectal Smooth Muscle	rectum
40	chr6:25174200-25175200	Enhancers	NHLF	lung
41	chr6:25174200-25175800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr6:25174200-25176200	Enhancers	Muscle Satellite Cultured Cells	--
43	chr6:25174200-25176600	Enhancers	Fetal Thymus	thymus
44	chr6:25174200-25177000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:25174400-25175200	Enhancers	Colonic Mucosa	Colon
46	chr6:25174600-25175800	Weak transcription	Colon Smooth Muscle	Colon
47	chr6:25174600-25175800	Weak transcription	Fetal Stomach	stomach
48	chr6:25174600-25175800	Enhancers	Gastric	stomach
49	chr6:25174600-25176200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr6:25174600-25176200	Enhancers	Lung	lung

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