Variant report

Variant	rs62538847
Chromosome Location	chr9:12957305-12957306
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	chr9:12955347..12957519-chr9:12959298..12960920,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10118051	0.99[ASN][1000 genomes]
rs10118083	0.99[ASN][1000 genomes]
rs10429589	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10429614	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10448183	0.98[ASN][1000 genomes]
rs10756431	0.99[ASN][1000 genomes]
rs10756432	0.99[ASN][1000 genomes]
rs10756433	0.99[ASN][1000 genomes]
rs10756434	0.99[ASN][1000 genomes]
rs10756435	0.99[ASN][1000 genomes]
rs10809863	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10809864	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10809865	0.99[ASN][1000 genomes]
rs10809866	0.99[ASN][1000 genomes]
rs10809867	0.99[ASN][1000 genomes]
rs10809868	0.99[ASN][1000 genomes]
rs10809869	0.99[ASN][1000 genomes]
rs10809870	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10960860	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10960861	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10960863	0.89[ASN][1000 genomes]
rs10960865	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10960866	0.98[ASN][1000 genomes]
rs10960868	0.98[ASN][1000 genomes]
rs1536788	0.81[EUR][1000 genomes]
rs1536789	0.80[ASN][1000 genomes]
rs2026716	0.99[ASN][1000 genomes]
rs2065424	0.92[ASN][1000 genomes]
rs2183133	0.99[ASN][1000 genomes]
rs2382383	0.84[ASN][1000 genomes]
rs3932596	0.99[ASN][1000 genomes]
rs4587431	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4740538	0.99[ASN][1000 genomes]
rs4741261	0.99[ASN][1000 genomes]
rs4741262	0.99[ASN][1000 genomes]
rs4741263	0.99[ASN][1000 genomes]
rs58120442	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62538846	0.92[ASN][1000 genomes]
rs7859146	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498136	chr9:12387840-12984158	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv613616	chr9:12922330-13018096	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv892576	chr9:12925921-13093345	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv466258	chr9:12928475-12968196	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv613617	chr9:12928475-12968196	Weak transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv892577	chr9:12928475-12995112	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv917331	chr9:12941193-13146852	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv892578	chr9:12942956-13485035	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv892579	chr9:12954161-13120380	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 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	chr9:12951400-12958400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:12954400-12957800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:12955000-12957600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr9:12956000-12958400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:12956200-12957800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr9:12956600-12957600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr9:12956600-12957800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr9:12956600-12957800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr9:12956800-12958000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr9:12957000-12961200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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