Variant report

Variant	rs652088
Chromosome Location	chr21:41013909-41013910
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	chr21:41004099..41006698-chr21:41012872..41015470,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs490561	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs498027	0.86[JPT][hapmap]
rs591524	0.86[JPT][hapmap]
rs608229	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs609145	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs610353	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs679857	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs760165	0.87[JPT][hapmap]

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	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1057956	chr21:40907707-41393396	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv544444	chr21:40907707-41393396	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv459260	chr21:41000353-41028197	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv587485	chr21:41000353-41028197	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40998200-41014800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr21:41007800-41017400	Enhancers	Fetal Intestine Small	intestine
3	chr21:41008200-41017200	Enhancers	Fetal Intestine Large	intestine
4	chr21:41008200-41017400	Enhancers	Stomach Mucosa	stomach
5	chr21:41008800-41015600	Weak transcription	HSMMtube	muscle
6	chr21:41009000-41018200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr21:41009400-41015800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr21:41010800-41015000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr21:41010800-41015400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr21:41011000-41014000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr21:41011000-41015000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr21:41011000-41015400	Weak transcription	HSMM	muscle
13	chr21:41011000-41015600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr21:41011000-41015600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr21:41011000-41015600	Weak transcription	Colonic Mucosa	Colon
16	chr21:41011000-41016400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr21:41011200-41014400	Enhancers	Rectal Mucosa Donor 29	rectum
18	chr21:41011200-41015400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr21:41011200-41015600	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr21:41011200-41019000	Weak transcription	NH-A	brain
21	chr21:41012800-41014800	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr21:41012800-41015200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr21:41013000-41014400	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr21:41013000-41014800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr21:41013000-41015200	Weak transcription	Pancreas	Pancrea
26	chr21:41013000-41039000	Weak transcription	Gastric	stomach
27	chr21:41013000-41041800	Weak transcription	Small Intestine	intestine
28	chr21:41013400-41014000	Enhancers	Fetal Lung	lung
29	chr21:41013400-41017000	Active TSS	Duodenum Mucosa	Duodenum
30	chr21:41013600-41014000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr21:41013600-41014200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr21:41013600-41014200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr21:41013600-41014400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr21:41013600-41014400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr21:41013800-41014000	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr21:41013800-41014200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr21:41013800-41014400	Enhancers	H9 Cell Line	embryonic stem cell
38	chr21:41013800-41014400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr21:41013800-41017600	Enhancers	H1 Cell Line	embryonic stem cell

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