Variant report

Variant	rs1412298
Chromosome Location	chr9:12959510-12959511
allele	C/G
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: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10465043	1.00[EUR][1000 genomes]
rs10738307	1.00[EUR][1000 genomes]
rs13289590	0.80[EUR][1000 genomes]
rs13289610	0.80[EUR][1000 genomes]
rs13290445	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13291242	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13291883	0.80[EUR][1000 genomes]
rs13296015	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34668426	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34948391	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35205602	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35380238	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35659791	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35803051	0.80[EUR][1000 genomes]
rs36076364	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4740537	1.00[EUR][1000 genomes]
rs4741259	0.86[EUR][1000 genomes]
rs4741264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7031108	0.80[EUR][1000 genomes]
rs71474400	0.80[EUR][1000 genomes]
rs71507352	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71507353	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71507354	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7855889	1.00[EUR][1000 genomes]
rs7856120	0.80[EUR][1000 genomes]
rs7866189	0.80[EUR][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:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12957000-12961200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr9:12957600-12959600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
3	chr9:12957800-12959600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
4	chr9:12958200-12959600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
5	chr9:12958600-12961400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr9:12958800-12965400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:12959000-12960200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
8	chr9:12959000-12961200	Weak transcription	Fetal Lung	lung
9	chr9:12959200-12961200	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr9:12959200-12962400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:12959400-12960400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr9:12959400-12963600	Weak transcription	Liver	Liver

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