Variant report

Variant	rs6459021
Chromosome Location	chr6:54588069-54588070
allele	A/G
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:54562310..54563986-chr6:54587468..54589771,2	MCF-7	breast:
2	chr6:54587916..54591176-chr6:54736715..54740306,4	MCF-7	breast:
3	chr6:54573340..54575837-chr6:54587895..54589989,2	MCF-7	breast:
4	chr6:54561293..54570100-chr6:54582505..54590247,14	MCF-7	breast:
5	chr6:54581587..54585941-chr6:54586924..54591451,7	MCF-7	breast:
6	chr6:54580831..54596896-chr6:54704751..54716103,89	MCF-7	breast:
7	chr6:54586929..54589873-chr6:54742420..54744071,2	MCF-7	breast:
8	chr6:54585837..54588493-chr6:54594744..54597239,2	MCF-7	breast:
9	chr6:54577593..54590845-chr6:54708062..54715554,67	MCF-7	breast:
10	chr6:54564726..54568882-chr6:54587061..54590275,4	MCF-7	breast:
11	chr6:54586807..54589626-chr6:54590506..54593407,2	MCF-7	breast:
12	chr6:54585158..54588149-chr6:54741239..54743201,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction
ENSG00000224984	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1039693	0.85[CEU][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap]
rs10447377	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs10807475	0.81[ASN][1000 genomes]
rs10948830	0.80[ASN][1000 genomes]
rs10948842	0.97[ASN][1000 genomes]
rs11757171	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs11964037	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12211545	0.97[ASN][1000 genomes]
rs12215844	0.87[ASN][1000 genomes]
rs13193002	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13200833	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13217514	0.85[CEU][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1359009	0.84[ASN][1000 genomes]
rs1911508	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2089411	0.95[ASN][1000 genomes]
rs2174145	0.96[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2174735	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2297804	0.85[CEU][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs6899853	0.85[CEU][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs6908136	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6916681	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6918290	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72967406	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs925057	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9464114	0.84[ASN][1000 genomes]
rs9464116	0.91[ASN][1000 genomes]
rs9464135	0.83[EUR][1000 genomes]
rs9474940	0.84[ASN][1000 genomes]
rs9474943	0.84[ASN][1000 genomes]
rs9474944	0.87[ASN][1000 genomes]
rs9474965	0.86[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9474972	0.85[CEU][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs9474973	0.89[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9474974	0.81[ASN][1000 genomes]
rs9474977	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9474987	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9474991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs981682	0.85[CEU][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs9885668	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs995951	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[MKK][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	nsv885901	chr6:54588069-54635417	Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv885902	chr6:54588069-54656673	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54583600-54594200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr6:54587200-54594200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:54587400-54594200	Weak transcription	NHEK	skin

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