Variant report

Variant	rs669728
Chromosome Location	chr6:56265383-56265384
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56252272..56255163-chr6:56263455..56266276,3	MCF-7	breast:
2	chr6:56263704..56266113-chr6:56287391..56289066,2	MCF-7	breast:
3	chr6:56263868..56266502-chr6:56269861..56271738,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1008768	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1008769	0.90[CHB][hapmap];0.96[JPT][hapmap];0.88[ASN][1000 genomes]
rs1008770	0.89[ASN][1000 genomes]
rs1014740	0.97[ASN][1000 genomes]
rs1018414	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1018415	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11968073	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12205291	0.88[ASN][1000 genomes]
rs12528936	0.97[ASN][1000 genomes]
rs13206552	0.90[CHB][hapmap];0.96[JPT][hapmap];0.89[ASN][1000 genomes]
rs2143349	0.85[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs2179519	0.97[ASN][1000 genomes]
rs2206528	1.00[CHB][hapmap];0.96[JPT][hapmap];0.96[ASN][1000 genomes]
rs2206530	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2397222	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2894836	0.91[ASN][1000 genomes]
rs35253323	0.95[ASN][1000 genomes]
rs4715621	0.97[ASN][1000 genomes]
rs4715624	0.95[ASN][1000 genomes]
rs629057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643246	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs646884	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs669656	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs926530	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9296843	0.97[ASN][1000 genomes]
rs9349821	0.97[ASN][1000 genomes]
rs9370527	0.90[CHB][hapmap];0.96[JPT][hapmap];0.89[ASN][1000 genomes]
rs9370530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9382625	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9382627	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9382630	0.95[ASN][1000 genomes]
rs9396208	0.97[ASN][1000 genomes]
rs9396209	0.97[ASN][1000 genomes]
rs9942454	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830666	chr6:56243743-56419599	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1022577	chr6:56263674-56289698	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv12046	chr6:56265335-56265821	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56253000-56282600	Weak transcription	Aorta	Aorta
2	chr6:56261800-56265600	Enhancers	Fetal Intestine Large	intestine
3	chr6:56263400-56265600	Enhancers	Fetal Intestine Small	intestine
4	chr6:56263800-56265400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
5	chr6:56264200-56265400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:56264200-56265400	Enhancers	Pancreas	Pancrea
7	chr6:56264200-56265800	Active TSS	Duodenum Mucosa	Duodenum
8	chr6:56264400-56268600	Weak transcription	Small Intestine	intestine
9	chr6:56264600-56265600	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr6:56264800-56265400	Enhancers	Gastric	stomach
11	chr6:56264800-56265800	Flanking Active TSS	HepG2	liver
12	chr6:56265000-56265400	Flanking Active TSS	A549	lung
13	chr6:56265200-56265400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:56265200-56265400	Active TSS	Liver	Liver
15	chr6:56265200-56265400	Enhancers	Fetal Kidney	kidney
16	chr6:56265200-56265600	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr6:56265200-56268600	Weak transcription	Hela-S3	cervix
18	chr6:56265200-56270000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:56265200-56270200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:56265200-56271200	Weak transcription	Stomach Mucosa	stomach

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