Variant report

Variant	rs9474972
Chromosome Location	chr6:54586637-54586638
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:54585487..54587893-chr6:54738565..54741108,3	MCF-7	breast:
2	chr6:54584974..54587110-chr6:54788503..54790985,2	MCF-7	breast:
3	chr6:54561293..54570100-chr6:54582505..54590247,14	MCF-7	breast:
4	chr6:54580831..54596896-chr6:54704751..54716103,89	MCF-7	breast:
5	chr6:54585837..54588493-chr6:54594744..54597239,2	MCF-7	breast:
6	chr6:54577593..54590845-chr6:54708062..54715554,67	MCF-7	breast:
7	chr6:54585158..54588149-chr6:54741239..54743201,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction
ENSG00000224984	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1039693	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10948842	0.80[ASN][1000 genomes]
rs11964037	0.81[ASN][1000 genomes]
rs12211545	0.80[ASN][1000 genomes]
rs13193002	0.81[CEU][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs13217514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1911508	0.83[ASN][1000 genomes]
rs2174145	0.82[CEU][hapmap]
rs2174735	0.81[ASN][1000 genomes]
rs2297804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6459021	0.85[CEU][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs6899853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6908136	0.83[ASN][1000 genomes]
rs6914808	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6916681	0.80[CEU][hapmap]
rs6929108	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs925057	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs9464124	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9474965	0.82[ASN][1000 genomes]
rs9474973	0.83[ASN][1000 genomes]
rs9474974	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9474977	0.81[ASN][1000 genomes]
rs9474987	0.81[ASN][1000 genomes]
rs9474991	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs981682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9885668	0.80[ASN][1000 genomes]
rs995951	0.82[JPT][hapmap];0.83[ASN][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:6 , 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	chr6:54585200-54587200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr6:54586400-54587200	Enhancers	HMEC	breast
4	chr6:54586600-54587200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:54586600-54587400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:54586600-54587400	Enhancers	NHEK	skin

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