Variant report

Variant	rs7961562
Chromosome Location	chr12:67464708-67464709
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:67448355..67449925-chr12:67462962..67464949,2	MCF-7	breast:
2	chr12:67310671..67312914-chr12:67463080..67465006,2	MCF-7	breast:
3	chr12:67427801..67429631-chr12:67463165..67465076,2	MCF-7	breast:
4	chr12:67463389..67464966-chr12:67474386..67476237,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10459266	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10784605	0.91[ASN][1000 genomes]
rs10784606	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10784607	0.91[ASN][1000 genomes]
rs10784608	0.91[ASN][1000 genomes]
rs10784609	0.91[ASN][1000 genomes]
rs10878553	0.88[ASN][1000 genomes]
rs10878559	0.91[ASN][1000 genomes]
rs10878560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10878561	0.91[ASN][1000 genomes]
rs10878566	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1104655	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11176552	0.88[ASN][1000 genomes]
rs11176555	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs11176556	0.86[ASN][1000 genomes]
rs11176557	0.91[ASN][1000 genomes]
rs11176562	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11176567	0.95[ASN][1000 genomes]
rs11176577	0.84[ASN][1000 genomes]
rs11176580	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11176582	0.89[ASN][1000 genomes]
rs11176586	0.91[ASN][1000 genomes]
rs11829047	0.91[ASN][1000 genomes]
rs12227624	0.91[ASN][1000 genomes]
rs12227692	0.95[ASN][1000 genomes]
rs12228046	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12228922	0.91[ASN][1000 genomes]
rs12228998	0.93[ASN][1000 genomes]
rs12230670	0.91[ASN][1000 genomes]
rs12231102	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12833688	0.91[ASN][1000 genomes]
rs1465026	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1526835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1526839	0.91[ASN][1000 genomes]
rs1589971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17183558	0.81[CEU][hapmap]
rs17183565	0.81[CEU][hapmap]
rs2870926	0.88[ASN][1000 genomes]
rs2904534	0.88[ASN][1000 genomes]
rs4244070	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4913529	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6581735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581740	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7136952	0.88[ASN][1000 genomes]
rs7138249	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7298268	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7311137	0.93[ASN][1000 genomes]
rs7953961	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7959866	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7961790	0.93[ASN][1000 genomes]
rs7961954	0.93[ASN][1000 genomes]
rs7962241	0.93[ASN][1000 genomes]
rs7974866	0.87[CEU][hapmap];0.91[ASN][1000 genomes]
rs7980101	0.93[ASN][1000 genomes]
rs941096	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv541524	chr12:67311057-67700349	Strong transcription Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv469462	chr12:67361657-67475906	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv559211	chr12:67361657-67475906	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv559212	chr12:67373549-67850925	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67464200-67464800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
2	chr12:67464400-67464800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
3	chr12:67464400-67464800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
4	chr12:67464400-67465000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:67464400-67465000	Enhancers	HMEC	breast
6	chr12:67464400-67468000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:67464400-67469000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:67464600-67464800	Bivalent Enhancer	Placenta	Placenta
9	chr12:67464600-67468000	Weak transcription	NHEK	skin
10	chr12:67464600-67469200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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