Variant report

Variant	rs1976539
Chromosome Location	chr6:54565541-54565542
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:54558970..54566519-chr6:54708534..54713743,16	MCF-7	breast:
2	chr6:54563782..54566701-chr6:54762502..54764565,2	MCF-7	breast:
3	chr6:54564442..54567295-chr6:54579442..54581907,3	MCF-7	breast:
4	chr6:54564646..54566812-chr6:54747166..54750251,3	MCF-7	breast:
5	chr6:54559522..54567174-chr6:54707552..54714330,37	MCF-7	breast:
6	chr6:54564726..54568882-chr6:54587061..54590275,4	MCF-7	breast:
7	chr6:54564170..54566593-chr6:54739128..54740974,2	MCF-7	breast:
8	chr6:54560120..54562700-chr6:54564068..54565878,2	MCF-7	breast:
9	chr6:54561293..54570100-chr6:54582505..54590247,14	MCF-7	breast:
10	chr6:54559803..54567776-chr6:54579525..54585377,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1039495	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1039496	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10948840	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10948844	0.83[ASN][1000 genomes]
rs10948846	0.86[ASN][1000 genomes]
rs12525539	0.92[EUR][1000 genomes]
rs12527042	0.83[ASN][1000 genomes]
rs12527077	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12527080	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12527124	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12528270	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12528881	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12529275	0.91[EUR][1000 genomes]
rs12661998	0.86[ASN][1000 genomes]
rs12662465	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1395624	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1648201	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16869519	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16885649	0.92[EUR][1000 genomes]
rs16885656	0.92[EUR][1000 genomes]
rs16885668	0.92[EUR][1000 genomes]
rs16885735	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16885866	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16885911	0.86[ASN][1000 genomes]
rs16885948	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1951693	0.82[EUR][1000 genomes]
rs2048112	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2894821	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34752465	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35953958	0.85[ASN][1000 genomes]
rs4712068	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4715468	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4715470	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4715478	0.85[ASN][1000 genomes]
rs4994100	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58302712	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60501416	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs608873	0.91[EUR][1000 genomes]
rs67799698	0.88[ASN][1000 genomes]
rs67875074	0.88[ASN][1000 genomes]
rs6915244	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73444113	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73444116	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73444125	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73446026	0.86[ASN][1000 genomes]
rs73446030	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73446036	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73446043	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7751908	0.92[EUR][1000 genomes]
rs7761021	0.91[EUR][1000 genomes]
rs9349726	0.91[EUR][1000 genomes]
rs9370323	0.82[EUR][1000 genomes]
rs9474957	0.85[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54564200-54571000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr6:54564400-54570800	Weak transcription	Stomach Mucosa	stomach
3	chr6:54564400-54575200	Weak transcription	Fetal Lung	lung
4	chr6:54565000-54565600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:54565000-54565600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:54565200-54565600	Enhancers	NHEK	skin
7	chr6:54565200-54566200	Weak transcription	Fetal Intestine Small	intestine
8	chr6:54565400-54575400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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