Variant report

Variant	rs17138543
Chromosome Location	chr6:4589963-4589964
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4587247..4590668-chr6:4591336..4594466,3	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11751457	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11756102	1.00[CEU][hapmap]
rs11962754	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11964426	1.00[CEU][hapmap]
rs17138527	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17138534	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143455	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2235724	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2235726	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2235727	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs377207	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs378901	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs382186	0.85[EUR][1000 genomes]
rs385236	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs385884	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs390126	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs390617	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs400405	0.91[ASN][1000 genomes]
rs413716	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs418563	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs420580	0.82[EUR][1000 genomes]
rs421930	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs424137	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs438021	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs453768	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4959306	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4960004	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4960005	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4960006	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4960009	0.81[EUR][1000 genomes]
rs601192	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62384944	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911463	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6913171	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7747007	0.82[EUR][1000 genomes]
rs84996	0.88[EUR][1000 genomes]
rs9328261	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9328262	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9392607	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9502199	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9502200	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9502202	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9502204	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9502205	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9502206	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9504151	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9504152	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9504154	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9504156	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9504159	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9504160	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9504163	0.83[EUR][1000 genomes]
rs9504165	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs9504166	0.82[EUR][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	esv3421990	chr6:4446933-4659639	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv830576	chr6:4447554-4610604	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv3366530	chr6:4471528-4865322	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv883415	chr6:4546491-4629654	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4581800-4590000	Enhancers	Placenta	Placenta
2	chr6:4582400-4595400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:4584400-4593800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr6:4587200-4593800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:4589400-4590000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:4589400-4590000	Enhancers	HMEC	breast
7	chr6:4589400-4590000	Enhancers	NHEK	skin
8	chr6:4589400-4590200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:4589600-4590000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:4589800-4590000	Enhancers	HSMMtube	muscle

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