Variant report

Variant	rs9472109
Chromosome Location	chr6:12587195-12587196
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ESR1	chr6:12586998-12587329	T-47D	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000234015	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10046276	1.00[EUR][1000 genomes]
rs11750980	1.00[EUR][1000 genomes]
rs11966877	1.00[EUR][1000 genomes]
rs12332919	1.00[EUR][1000 genomes]
rs1334306	1.00[EUR][1000 genomes]
rs1334307	1.00[EUR][1000 genomes]
rs2490446	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2490448	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2490450	1.00[EUR][1000 genomes]
rs2490451	1.00[EUR][1000 genomes]
rs2504866	1.00[EUR][1000 genomes]
rs2504889	1.00[EUR][1000 genomes]
rs2504893	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2504896	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2516229	1.00[EUR][1000 genomes]
rs2516230	1.00[EUR][1000 genomes]
rs2516236	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2516237	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57317303	1.00[EUR][1000 genomes]
rs59901827	1.00[EUR][1000 genomes]
rs60493852	1.00[EUR][1000 genomes]
rs60501074	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6458322	1.00[EUR][1000 genomes]
rs6900340	1.00[EUR][1000 genomes]
rs6916851	1.00[EUR][1000 genomes]
rs6928058	1.00[EUR][1000 genomes]
rs6933484	1.00[EUR][1000 genomes]
rs73356106	1.00[EUR][1000 genomes]
rs73356116	1.00[EUR][1000 genomes]
rs73356122	1.00[EUR][1000 genomes]
rs73356124	1.00[EUR][1000 genomes]
rs73722796	1.00[EUR][1000 genomes]
rs7738584	1.00[EUR][1000 genomes]
rs9462819	1.00[EUR][1000 genomes]
rs9462825	1.00[EUR][1000 genomes]
rs9462830	1.00[EUR][1000 genomes]
rs9462834	1.00[EUR][1000 genomes]
rs9471867	1.00[EUR][1000 genomes]
rs9471922	1.00[EUR][1000 genomes]
rs9471924	1.00[EUR][1000 genomes]
rs9472012	1.00[EUR][1000 genomes]
rs9472013	1.00[EUR][1000 genomes]
rs9472037	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9472110	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9472123	1.00[EUR][1000 genomes]
rs9472198	1.00[EUR][1000 genomes]
rs9717503	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470801	chr6:12559239-12666093	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3521000	chr6:12561306-13128519	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv3521001	chr6:12561306-13128519	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv462638	chr6:12569231-12651249	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv600991	chr6:12569231-12651249	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12574000-12594600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:12579400-12588200	Weak transcription	A549	lung
3	chr6:12580000-12592800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:12583000-12588600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:12584800-12587400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:12585000-12587400	Enhancers	Fetal Intestine Small	intestine
7	chr6:12585200-12587600	Enhancers	Fetal Intestine Large	intestine
8	chr6:12585800-12587600	Enhancers	NHEK	skin
9	chr6:12586000-12587200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr6:12586200-12587200	Enhancers	Duodenum Mucosa	Duodenum
11	chr6:12586400-12587200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:12586400-12587200	Weak transcription	Placenta	Placenta
13	chr6:12586400-12588400	Enhancers	HUVEC	blood vessel
14	chr6:12586400-12589800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:12586400-12595600	Weak transcription	Left Ventricle	heart
16	chr6:12586800-12587400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:12587000-12587200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:12587000-12587200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr6:12587000-12587200	Enhancers	Pancreas	Pancrea
20	chr6:12587000-12587200	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr6:12587000-12587400	Enhancers	H1 Cell Line	embryonic stem cell
22	chr6:12587000-12587400	Enhancers	HMEC	breast
23	chr6:12587000-12587600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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