Variant report

Variant	rs229039
Chromosome Location	chr21:28205573-28205574
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	chr21:28204779..28207131-chr21:28215983..28217765,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154734	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs229029	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs229032	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs229034	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs229036	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs229037	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2830538	0.81[ASN][1000 genomes]
rs2830542	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3017433	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs419895	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs453519	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066573	chr21:28096356-28374354	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1057400	chr21:28104936-28359948	Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv834068	chr21:28179670-28360808	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv3482	chr21:28191297-28221975	Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
5	nsv470897	chr21:28196045-28216066	Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:28199000-28208400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr21:28199200-28208800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr21:28199400-28205600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr21:28199800-28208800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr21:28200600-28205800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr21:28200600-28205800	Weak transcription	HMEC	breast
7	chr21:28200600-28208800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr21:28203200-28209000	Enhancers	Dnd41	blood
9	chr21:28203600-28207800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr21:28204000-28210000	Weak transcription	HUVEC	blood vessel
11	chr21:28204200-28206400	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr21:28204600-28209000	Weak transcription	Brain Angular Gyrus	brain
13	chr21:28205000-28205600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr21:28205000-28206600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr21:28205200-28206000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr21:28205200-28206400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr21:28205200-28206800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr21:28205400-28205600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
19	chr21:28205400-28205800	Enhancers	Fetal Heart	heart
20	chr21:28205400-28205800	Enhancers	Placenta	Placenta
21	chr21:28205400-28206600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr21:28205400-28209000	Enhancers	NHEK	skin
23	chr21:28205400-28210000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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