Variant report

Variant	rs6769012
Chromosome Location	chr3:85982380-85982381
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	chr3:85963263..85965350-chr3:85981290..85983775,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10084716	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11715949	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12494511	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12636273	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12714642	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13068185	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13085195	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2324973	0.87[AMR][1000 genomes]
rs2324981	0.87[AMR][1000 genomes]
rs3906942	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4129497	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4302393	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4302394	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4308293	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4364177	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4488844	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4856606	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4856607	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56282418	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6549063	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6762937	0.83[EUR][1000 genomes]
rs6782553	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6787901	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6796380	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6796402	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6798987	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7426412	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7609709	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7614073	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7620544	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7626873	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7630752	0.87[AMR][1000 genomes]
rs7632162	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7636206	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7640041	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7642281	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7648895	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650420	0.82[AMR][1000 genomes]
rs9309996	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9310000	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9713674	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9810861	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9824085	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9824980	0.82[EUR][1000 genomes]
rs9829446	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9832847	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9841158	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9846878	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9850482	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9851502	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9875386	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9985228	0.86[EUR][1000 genomes]
rs9985441	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532629	chr3:85763873-86608579	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv877106	chr3:85814620-86006210	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv877107	chr3:85814620-86037162	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv877108	chr3:85870363-86037162	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
5	nsv877109	chr3:85892098-86006210	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
6	nsv877110	chr3:85892098-86037162	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
7	nsv877111	chr3:85892098-86044224	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
8	nsv460754	chr3:85917289-86006210	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
9	nsv460755	chr3:85917289-86006210	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
10	nsv590912	chr3:85917289-86006210	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
11	nsv470727	chr3:85917289-86044224	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
12	nsv590913	chr3:85917289-86044224	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
13	nsv877112	chr3:85964737-86083716	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85965200-85987000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:85981600-85988200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:85982200-85982400	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr3:85982200-85982400	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr3:85982200-85982800	Enhancers	H9 Cell Line	embryonic stem cell
6	chr3:85982200-85983800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:85982200-85984000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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