Variant report

Variant	rs28859986
Chromosome Location	chr3:83368013-83368014
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	chr3:83367096..83369099-chr3:83414671..83417378,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12714565	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12714566	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13061386	0.87[EUR][1000 genomes]
rs1452167	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1551232	0.87[EUR][1000 genomes]
rs164273	0.89[EUR][1000 genomes]
rs2198281	0.89[EUR][1000 genomes]
rs28893195	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs398555	0.89[EUR][1000 genomes]
rs67529822	0.87[EUR][1000 genomes]
rs67764414	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs700013	0.89[EUR][1000 genomes]
rs7648751	0.87[EUR][1000 genomes]
rs9811230	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9811656	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9812521	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9842201	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9843358	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9848958	0.89[EUR][1000 genomes]
rs9865924	0.86[EUR][1000 genomes]
rs9867218	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9869072	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9878614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9882209	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008268	chr3:83057096-83476080	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv536608	chr3:83057096-83476080	Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv998408	chr3:83057096-83549271	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv536609	chr3:83057096-83549271	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv3324557	chr3:83153978-83450434	Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv470694	chr3:83154414-83425479	Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv877069	chr3:83216023-83425480	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv877071	chr3:83324183-83536528	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 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	chr3:83366600-83369400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:83367600-83370600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:83368000-83370200	Enhancers	Dnd41	blood

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