Variant report

Variant	rs28546473
Chromosome Location	chr4:78982692-78982693
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:78982293..78984651-chr4:78992521..78995488,2	MCF-7	breast:
2	chr4:78980938..78982697-chr4:79002374..79004588,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10000964	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10005124	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10016866	1.00[ASN][1000 genomes]
rs1502887	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17002912	0.90[EUR][1000 genomes]
rs17002918	0.90[EUR][1000 genomes]
rs17002919	0.90[EUR][1000 genomes]
rs17002923	0.88[EUR][1000 genomes]
rs28366819	0.90[EUR][1000 genomes]
rs28367528	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28446054	0.90[EUR][1000 genomes]
rs28477353	0.88[EUR][1000 genomes]
rs28497565	0.88[EUR][1000 genomes]
rs28520643	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28566614	0.88[EUR][1000 genomes]
rs28723619	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4340818	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6533375	1.00[ASN][1000 genomes]
rs6842322	1.00[ASN][1000 genomes]
rs72858745	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72858775	0.88[EUR][1000 genomes]
rs9284616	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9284617	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307331	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][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	nsv1010714	chr4:78742505-78991030	Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78980800-78983000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:78980800-78983000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:78980800-78990000	Weak transcription	NHDF-Ad	bronchial
4	chr4:78980800-78990600	Weak transcription	Psoas Muscle	Psoas
5	chr4:78980800-78998200	Weak transcription	Pancreas	Pancrea
6	chr4:78981000-78983000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:78981000-78983000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:78981000-78984400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr4:78981000-78984800	Enhancers	Fetal Heart	heart
10	chr4:78981000-78990600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:78981000-78991200	Weak transcription	Right Atrium	heart
12	chr4:78981000-78995600	Weak transcription	Fetal Intestine Small	intestine
13	chr4:78981200-79016600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:78981400-78982800	Weak transcription	NHEK	skin
15	chr4:78981400-78984000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr4:78981400-78986600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:78981400-78990400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr4:78981600-78985400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:78981600-78986600	Weak transcription	Fetal Intestine Large	intestine
20	chr4:78981800-78982800	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr4:78981800-78982800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:78981800-78983400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr4:78981800-78984400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:78981800-78986600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:78981800-78987000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr4:78982000-78983200	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr4:78982000-78984400	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr4:78982000-78984800	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr4:78982000-78984800	Enhancers	HepG2	liver
30	chr4:78982200-78982800	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr4:78982200-78983400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr4:78982200-78990600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr4:78982200-78998200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr4:78982600-78984600	Enhancers	HMEC	breast
35	chr4:78982600-78984800	Enhancers	H1 Cell Line	embryonic stem cell

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