Variant report

Variant	rs28550894
Chromosome Location	chr4:93256223-93256224
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	chr4:93254754..93257584-chr4:93259309..93261079,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10009241	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10012379	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10015916	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10016309	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10032538	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516906	0.84[EUR][1000 genomes]
rs13121565	0.92[EUR][1000 genomes]
rs13123172	0.84[EUR][1000 genomes]
rs13143394	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13150879	0.92[EUR][1000 genomes]
rs1513454	0.91[ASN][1000 genomes]
rs1513456	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1513462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1513467	0.92[EUR][1000 genomes]
rs17019289	0.90[ASN][1000 genomes]
rs17019295	0.94[ASN][1000 genomes]
rs17019316	0.94[ASN][1000 genomes]
rs17019318	0.94[ASN][1000 genomes]
rs17019329	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17238193	0.92[EUR][1000 genomes]
rs17238679	0.92[EUR][1000 genomes]
rs17317393	0.92[EUR][1000 genomes]
rs17619771	0.92[EUR][1000 genomes]
rs1877598	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2175767	0.90[EUR][1000 genomes]
rs28396937	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28429309	0.91[ASN][1000 genomes]
rs28864996	0.84[ASN][1000 genomes]
rs34742978	0.92[EUR][1000 genomes]
rs35214260	0.84[EUR][1000 genomes]
rs35358234	0.87[EUR][1000 genomes]
rs36116627	0.92[EUR][1000 genomes]
rs36123040	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62310971	0.86[EUR][1000 genomes]
rs62310990	0.86[EUR][1000 genomes]
rs62310993	0.86[EUR][1000 genomes]
rs62310994	0.87[EUR][1000 genomes]
rs62311001	0.92[EUR][1000 genomes]
rs6812781	0.92[ASN][1000 genomes]
rs6824860	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848132	0.92[EUR][1000 genomes]
rs6848674	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7692631	0.91[ASN][1000 genomes]
rs951961	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs951962	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9884958	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9990511	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530154	chr4:92396539-93359983	Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1009960	chr4:92747531-93389054	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv470056	chr4:92837584-93322977	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv461587	chr4:92837584-93376231	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv594866	chr4:92837584-93376231	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv948712	chr4:93007985-93740409	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv879603	chr4:93053028-93276174	ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv879604	chr4:93064187-93287744	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv830007	chr4:93101912-93317656	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv594868	chr4:93190198-93391251	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv998246	chr4:93198845-93350325	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	esv1835393	chr4:93222515-93276174	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:93253600-93282600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:93254000-93256400	Enhancers	Fetal Heart	heart
3	chr4:93254200-93263200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr4:93254400-93259400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr4:93254600-93259000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:93254600-93260000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:93254600-93260200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr4:93255200-93256600	Enhancers	Fetal Lung	lung
9	chr4:93255200-93256800	Enhancers	Colon Smooth Muscle	Colon
10	chr4:93255400-93256600	Enhancers	Fetal Stomach	stomach
11	chr4:93256000-93256600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr4:93256000-93261000	Weak transcription	Brain Germinal Matrix	brain
13	chr4:93256200-93256600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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