Variant report

Variant	rs9475080
Chromosome Location	chr6:54813509-54813510
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:54810051..54812419-chr6:54813190..54815495,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HMGCLL1-2	chr6:54813398-54813612	NONHSAT113230

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10485135	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10948865	1.00[EUR][1000 genomes]
rs10948871	0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11961881	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11964483	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1507112	1.00[EUR][1000 genomes]
rs16886234	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16886244	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16886248	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16886267	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2062780	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2062781	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4327697	1.00[EUR][1000 genomes]
rs4428489	1.00[EUR][1000 genomes]
rs55644513	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55954156	1.00[EUR][1000 genomes]
rs57287621	1.00[EUR][1000 genomes]
rs58495896	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60013096	1.00[EUR][1000 genomes]
rs60517516	1.00[EUR][1000 genomes]
rs61632434	1.00[EUR][1000 genomes]
rs6906651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6915116	1.00[EUR][1000 genomes]
rs6933855	1.00[EUR][1000 genomes]
rs73431481	1.00[EUR][1000 genomes]
rs73432338	1.00[EUR][1000 genomes]
rs73432360	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73432383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73434410	1.00[EUR][1000 genomes]
rs73446382	1.00[EUR][1000 genomes]
rs73742854	1.00[EUR][1000 genomes]
rs73742861	1.00[EUR][1000 genomes]
rs73742862	1.00[EUR][1000 genomes]
rs73742869	1.00[EUR][1000 genomes]
rs7756856	1.00[EUR][1000 genomes]
rs7772366	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9296772	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9464150	1.00[EUR][1000 genomes]
rs9464164	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9464165	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9464168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9464169	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9464170	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475070	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475071	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475074	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475076	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475084	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475086	0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54798800-54815600	Weak transcription	Fetal Intestine Small	intestine
2	chr6:54807400-54818000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:54807800-54815200	Weak transcription	NHEK	skin
4	chr6:54809400-54817600	Weak transcription	HMEC	breast
5	chr6:54809600-54814200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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