Variant report

Variant	rs3024805
Chromosome Location	chr2:85891264-85891265
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:85889712..85892300-chr2:85895263..85898036,2	MCF-7	breast:
2	chr2:85886996..85889867-chr2:85891019..85894482,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168878	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs3024803	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3024810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3024811	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3024815	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs3024818	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs3024819	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs3024822	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs3024827	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs3024828	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs57175088	1.00[AMR][1000 genomes]
rs57762218	0.87[AMR][1000 genomes]
rs57789237	1.00[AMR][1000 genomes]
rs59048598	0.87[AMR][1000 genomes]
rs59227664	0.87[AMR][1000 genomes]
rs60661938	0.87[AMR][1000 genomes]
rs60755293	0.87[AMR][1000 genomes]
rs60801683	0.87[AMR][1000 genomes]
rs61535370	0.87[AMR][1000 genomes]
rs61536745	0.87[AMR][1000 genomes]
rs6718028	0.87[AMR][1000 genomes]
rs72923039	0.87[AMR][1000 genomes]
rs72923051	0.87[AMR][1000 genomes]
rs72923062	0.87[AMR][1000 genomes]
rs72923064	0.87[AMR][1000 genomes]
rs72923077	0.87[AMR][1000 genomes]
rs72923080	0.87[AMR][1000 genomes]
rs72923082	0.87[AMR][1000 genomes]
rs7564769	0.87[AMR][1000 genomes]
rs7579847	0.87[AMR][1000 genomes]
rs7580358	1.00[AMR][1000 genomes]
rs7584055	1.00[AMR][1000 genomes]
rs7589436	1.00[AMR][1000 genomes]
rs7599812	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874459	chr2:85828014-85939207	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv874460	chr2:85828014-85941074	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv874461	chr2:85853653-85939207	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv874462	chr2:85853653-85941074	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv874463	chr2:85853653-85946708	Strong transcription Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv874464	chr2:85886175-85898898	Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85876600-85895400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:85877200-85893200	Weak transcription	Brain Substantia Nigra	brain
3	chr2:85878800-85891400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:85879600-85894000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:85879600-85896000	Weak transcription	GM12878-XiMat	blood
6	chr2:85880400-85891800	Weak transcription	HepG2	liver
7	chr2:85881800-85895800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:85883600-85892800	Weak transcription	Fetal Lung	lung
9	chr2:85883600-85900000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr2:85884800-85895600	Weak transcription	Primary B cells from cord blood	blood
11	chr2:85884800-85896600	Weak transcription	Primary B cells from peripheral blood	blood
12	chr2:85886400-85893200	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr2:85886400-85901000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:85887000-85891600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:85887000-85892600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:85887000-85896200	Weak transcription	Fetal Brain Female	brain
17	chr2:85887000-85905800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr2:85887200-85891400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:85887200-85895200	Weak transcription	Fetal Thymus	thymus
20	chr2:85887400-85891400	Weak transcription	Fetal Intestine Small	intestine
21	chr2:85887400-85893600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:85888000-85891400	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr2:85888600-85891400	Enhancers	NHLF	lung
24	chr2:85888600-85893200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr2:85888800-85891600	Enhancers	Left Ventricle	heart
26	chr2:85888800-85893000	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr2:85888800-85893000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr2:85889000-85893400	Weak transcription	Spleen	Spleen
29	chr2:85889200-85891400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:85889200-85892200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:85889200-85894200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:85889400-85891400	Weak transcription	Thymus	Thymus
33	chr2:85889400-85893400	Weak transcription	Colonic Mucosa	Colon
34	chr2:85890000-85894000	Transcr. at gene 5' and 3'	Lung	lung
35	chr2:85890200-85891400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:85890200-85893000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr2:85890200-85896400	Weak transcription	Pancreas	Pancrea
38	chr2:85890400-85891800	Weak transcription	Brain Anterior Caudate	brain
39	chr2:85890400-85893800	Weak transcription	Placenta	Placenta
40	chr2:85890600-85895400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:85890800-85893000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr2:85890800-85895000	Weak transcription	Osteobl	bone
43	chr2:85890800-85895200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:85890800-85895200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:85890800-85895200	Weak transcription	A549	lung
46	chr2:85890800-85895400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:85890800-85895600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr2:85890800-85895800	Weak transcription	NH-A	brain
49	chr2:85891000-85905800	Weak transcription	Right Atrium	heart
50	chr2:85891200-85895000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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