Variant report

Variant	rs6969235
Chromosome Location	chr7:3849416-3849417
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	chr7:3848437..3851053-chr7:3868632..3870528,2	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10085400	0.82[ASN][1000 genomes]
rs10085568	0.82[ASN][1000 genomes]
rs10246449	0.82[ASN][1000 genomes]
rs10252169	0.82[ASN][1000 genomes]
rs10256741	0.82[ASN][1000 genomes]
rs10479833	0.87[ASN][1000 genomes]
rs10479834	0.87[ASN][1000 genomes]
rs10480105	0.87[ASN][1000 genomes]
rs10951315	0.81[ASN][1000 genomes]
rs10951322	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10951336	0.87[ASN][1000 genomes]
rs11976915	0.89[ASN][1000 genomes]
rs11977993	0.89[ASN][1000 genomes]
rs12112335	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12531980	0.87[ASN][1000 genomes]
rs12532040	0.85[ASN][1000 genomes]
rs12532903	0.89[ASN][1000 genomes]
rs12532912	0.89[ASN][1000 genomes]
rs12535195	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12536445	0.81[ASN][1000 genomes]
rs12536663	0.87[ASN][1000 genomes]
rs12537696	0.87[ASN][1000 genomes]
rs12538997	0.87[ASN][1000 genomes]
rs12540101	0.89[ASN][1000 genomes]
rs12540220	0.92[ASN][1000 genomes]
rs12701219	0.87[ASN][1000 genomes]
rs12701221	0.89[ASN][1000 genomes]
rs12701227	0.85[ASN][1000 genomes]
rs12701229	0.89[ASN][1000 genomes]
rs13221624	0.89[ASN][1000 genomes]
rs13236653	0.87[ASN][1000 genomes]
rs13236719	0.89[ASN][1000 genomes]
rs1548612	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2097900	0.87[ASN][1000 genomes]
rs2341959	0.89[ASN][1000 genomes]
rs2880204	0.87[ASN][1000 genomes]
rs34614163	0.87[ASN][1000 genomes]
rs34960833	0.87[ASN][1000 genomes]
rs35261333	0.87[ASN][1000 genomes]
rs35712888	0.89[ASN][1000 genomes]
rs41873	0.85[ASN][1000 genomes]
rs6462361	0.87[ASN][1000 genomes]
rs67665990	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6944479	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6945778	0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6948552	0.82[ASN][1000 genomes]
rs6953036	0.87[ASN][1000 genomes]
rs6953604	0.85[ASN][1000 genomes]
rs6957166	0.82[ASN][1000 genomes]
rs6957676	0.82[ASN][1000 genomes]
rs6961230	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6966030	0.89[ASN][1000 genomes]
rs6969052	0.81[ASN][1000 genomes]
rs6978964	0.87[ASN][1000 genomes]
rs6979937	0.87[ASN][1000 genomes]
rs6980085	0.87[ASN][1000 genomes]
rs7778705	0.87[ASN][1000 genomes]
rs7788747	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7794504	0.85[ASN][1000 genomes]
rs7806494	0.87[ASN][1000 genomes]
rs7807003	0.87[ASN][1000 genomes]
rs7811839	0.89[ASN][1000 genomes]
rs7811894	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs917198	0.87[ASN][1000 genomes]
rs985186	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018173	chr7:3258989-3879848	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv538660	chr7:3258989-3879848	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1016555	chr7:3298478-3872512	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv538661	chr7:3298478-3872512	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1021650	chr7:3665232-4577439	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1021443	chr7:3705273-3889334	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv2756505	chr7:3789992-3856544	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv605938	chr7:3792038-3852261	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1027624	chr7:3808366-3923408	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv538684	chr7:3808366-3923408	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv2762640	chr7:3838745-3856544	Enhancers Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3827000-3857200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:3830800-3859800	Weak transcription	Pancreas	Pancrea
3	chr7:3848400-3882000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr7:3848800-3849600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:3848800-3850200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr7:3848800-3851000	Enhancers	Fetal Stomach	stomach
7	chr7:3849000-3849800	Enhancers	H1 Cell Line	embryonic stem cell
8	chr7:3849000-3849800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:3849400-3849600	Enhancers	Fetal Muscle Trunk	muscle
10	chr7:3849400-3880600	Weak transcription	Aorta	Aorta

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