Variant report

Variant	rs200473
Chromosome Location	chr6:27765164-27765165
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:27100250..27106326-chr6:27760451..27766140,11	K562	blood:
2	chr6:27100655..27103990-chr6:27762026..27765564,3	K562	blood:
3	chr6:27104118..27107097-chr6:27763106..27766140,3	K562	blood:
4	chr6:27155042..27157581-chr6:27762343..27765282,2	K562	blood:
5	chr6:27113828..27116369-chr6:27762956..27765394,4	MCF-7	breast:
6	chr6:27112343..27120362-chr6:27757252..27765476,17	K562	blood:
7	chr6:27111619..27120059-chr6:27760198..27767915,14	K562	blood:
8	chr6:27763449..27765293-chr6:27766819..27768521,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000184825	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000196787	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1015075	0.85[JPT][hapmap]
rs12174918	0.91[ASN][1000 genomes]
rs175597	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs183225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200471	0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200478	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs200479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs200481	0.89[ASN][1000 genomes]
rs200482	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs200483	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs200484	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs200485	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs200488	0.85[ASN][1000 genomes]
rs200489	0.85[ASN][1000 genomes]
rs200490	1.00[JPT][hapmap]
rs200497	0.83[ASN][1000 genomes]
rs200498	0.81[ASN][1000 genomes]
rs200501	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs200948	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs200949	1.00[JPT][hapmap]
rs200950	0.81[ASN][1000 genomes]
rs200952	0.81[ASN][1000 genomes]
rs200953	1.00[JPT][hapmap]
rs200954	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs200965	1.00[JPT][hapmap]
rs200968	1.00[JPT][hapmap]
rs200973	1.00[JPT][hapmap]
rs200974	1.00[JPT][hapmap]
rs200975	1.00[JPT][hapmap]
rs200977	1.00[JPT][hapmap]
rs200981	1.00[JPT][hapmap]
rs200983	0.85[ASN][1000 genomes]
rs200989	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs200990	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs200992	0.83[ASN][1000 genomes]
rs200995	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs200996	0.85[ASN][1000 genomes]
rs201002	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2277104	0.83[ASN][1000 genomes]
rs2394001	0.91[ASN][1000 genomes]
rs2747054	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs34295134	0.85[ASN][1000 genomes]
rs36108923	0.85[ASN][1000 genomes]
rs370155	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs390764	0.87[ASN][1000 genomes]
rs401754	0.87[ASN][1000 genomes]
rs401763	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4713122	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4713124	0.91[ASN][1000 genomes]
rs480699	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56002038	0.87[EUR][1000 genomes]
rs56870390	0.85[ASN][1000 genomes]
rs59015666	0.91[ASN][1000 genomes]
rs59199903	0.87[EUR][1000 genomes]
rs666846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901437	0.87[EUR][1000 genomes]
rs6901712	0.87[EUR][1000 genomes]
rs6906980	0.81[EUR][1000 genomes]
rs6915101	0.87[EUR][1000 genomes]
rs6936952	0.87[EUR][1000 genomes]
rs6938018	0.87[EUR][1000 genomes]
rs904142	0.85[JPT][hapmap]
rs9348779	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9357052	1.00[JPT][hapmap]
rs9368531	0.87[ASN][1000 genomes]
rs9368534	0.83[ASN][1000 genomes]
rs9368535	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9368536	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9368537	0.85[JPT][hapmap]
rs9380018	0.89[ASN][1000 genomes]
rs9380026	1.00[JPT][hapmap]
rs9380028	0.85[JPT][hapmap]
rs9380030	0.85[JPT][hapmap]
rs9393858	0.87[ASN][1000 genomes]
rs9468227	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
3	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
4	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
5	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
6	nsv1017057	chr6:27745777-27789683	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	125 gene(s)	inside rSNPs	diseases
7	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs200473	Hs.158943	cis	multi-tissue	Pritchard

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27761200-27768600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr6:27761600-27768600	Weak transcription	NHEK	skin
3	chr6:27763400-27765600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:27764400-27766000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:27764400-27768400	Enhancers	K562	blood
6	chr6:27764400-27774200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr6:27764600-27768600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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