Variant report

Variant	rs12662079
Chromosome Location	chr6:78412412-78412413
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:78409901..78411994-chr6:78412184..78414411,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10498914	0.84[EUR][1000 genomes]
rs10943477	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12524278	0.84[EUR][1000 genomes]
rs12526572	0.81[EUR][1000 genomes]
rs12526967	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12527300	0.83[EUR][1000 genomes]
rs12528266	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12664392	0.91[ASN][1000 genomes]
rs12664974	0.99[ASN][1000 genomes]
rs12664999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12665272	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13194318	0.83[EUR][1000 genomes]
rs13198766	0.84[EUR][1000 genomes]
rs13199793	0.82[EUR][1000 genomes]
rs13204625	0.83[EUR][1000 genomes]
rs13219696	0.85[EUR][1000 genomes]
rs1483053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16889263	0.84[EUR][1000 genomes]
rs16889275	0.84[EUR][1000 genomes]
rs16889279	0.84[EUR][1000 genomes]
rs16889353	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1842899	0.83[ASN][1000 genomes]
rs1842900	0.83[ASN][1000 genomes]
rs1877532	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34107489	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34175887	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34515535	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34706559	0.84[EUR][1000 genomes]
rs34728195	0.85[EUR][1000 genomes]
rs34885141	0.84[EUR][1000 genomes]
rs35032650	0.84[EUR][1000 genomes]
rs35996314	0.82[EUR][1000 genomes]
rs4579319	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4708369	0.82[EUR][1000 genomes]
rs4708370	0.82[EUR][1000 genomes]
rs6454004	0.85[EUR][1000 genomes]
rs6454009	0.81[EUR][1000 genomes]
rs71563053	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71563056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71563070	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71563073	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7743545	0.81[EUR][1000 genomes]
rs9341700	0.81[EUR][1000 genomes]
rs9341701	0.81[EUR][1000 genomes]
rs9350725	0.85[EUR][1000 genomes]
rs9352524	0.85[EUR][1000 genomes]
rs9361281	0.85[EUR][1000 genomes]
rs9361299	0.81[EUR][1000 genomes]
rs9448209	0.84[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	nsv1034979	chr6:77781244-78426249	Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv538324	chr6:77781244-78426249	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1028259	chr6:78059491-78709871	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv538325	chr6:78059491-78709871	Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1031368	chr6:78335896-78503051	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv603812	chr6:78336806-78646748	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv2758063	chr6:78336955-78580830	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv2759446	chr6:78336955-78580830	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1016961	chr6:78352231-79003866	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv538326	chr6:78352231-79003866	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv949682	chr6:78355600-79002515	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	esv33879	chr6:78383851-78440074	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv5361	chr6:78401496-78457640	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:78410400-78413600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:78410400-78413600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:78410600-78412600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:78410800-78412800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:78411200-78412600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:78411800-78415000	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr6:78412200-78414800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr6:78412200-78414800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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