Variant report

Variant	rs6041773
Chromosome Location	chr20:13004149-13004150
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	chr20:13002186..13004190-chr20:13008427..13010353,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11907026	1.00[EUR][1000 genomes]
rs11907467	1.00[EUR][1000 genomes]
rs11908439	1.00[EUR][1000 genomes]
rs11908459	1.00[EUR][1000 genomes]
rs16993615	1.00[EUR][1000 genomes]
rs399107	1.00[EUR][1000 genomes]
rs473182	1.00[EUR][1000 genomes]
rs6033571	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6033580	1.00[EUR][1000 genomes]
rs6041745	1.00[EUR][1000 genomes]
rs6041746	1.00[EUR][1000 genomes]
rs6041754	1.00[EUR][1000 genomes]
rs6041756	1.00[EUR][1000 genomes]
rs6041778	1.00[EUR][1000 genomes]
rs7271965	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057219	chr20:12729479-13338337	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv912684	chr20:12734299-13311983	Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1067036	chr20:12737436-13338337	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv3488304	chr20:12738054-13341279	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv3488305	chr20:12738054-13341279	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv518184	chr20:12743808-13344672	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1063587	chr20:12756524-13330103	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv544185	chr20:12756524-13330103	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv916296	chr20:12756605-13329940	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv1067720	chr20:12756725-13329963	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv532513	chr20:12756725-13329963	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1064901	chr20:12773504-13318421	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv833923	chr20:12904689-13064426	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv833924	chr20:12997093-13189239	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:12997800-13008200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr20:13002200-13004200	Strong transcription	Fetal Intestine Large	intestine
3	chr20:13003000-13004200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr20:13003000-13006000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr20:13003400-13004600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr20:13003400-13015400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr20:13003600-13007800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr20:13003600-13010400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr20:13003600-13010400	Strong transcription	HepG2	liver
10	chr20:13003800-13005800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr20:13003800-13006000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr20:13003800-13006000	Weak transcription	Liver	Liver
13	chr20:13003800-13006600	Strong transcription	Placenta	Placenta
14	chr20:13003800-13007200	Weak transcription	Fetal Intestine Small	intestine
15	chr20:13003800-13007400	Weak transcription	Left Ventricle	heart
16	chr20:13003800-13008600	Weak transcription	NH-A	brain
17	chr20:13003800-13009200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr20:13003800-13009200	Weak transcription	Hela-S3	cervix
19	chr20:13003800-13009600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr20:13003800-13010400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr20:13003800-13014600	Weak transcription	Esophagus	oesophagus
22	chr20:13003800-13026400	Weak transcription	Aorta	Aorta
23	chr20:13003800-13049600	Weak transcription	Lung	lung
24	chr20:13004000-13005400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr20:13004000-13005600	Weak transcription	NHEK	skin
26	chr20:13004000-13005800	Weak transcription	HMEC	breast
27	chr20:13004000-13007200	Weak transcription	NHDF-Ad	bronchial
28	chr20:13004000-13007400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr20:13004000-13007400	Weak transcription	HSMM	muscle
30	chr20:13004000-13008600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr20:13004000-13008600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr20:13004000-13008600	Weak transcription	NHLF	lung
33	chr20:13004000-13008600	Weak transcription	Osteobl	bone
34	chr20:13004000-13010000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr20:13004000-13013000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr20:13004000-13027200	Weak transcription	Pancreas	Pancrea
37	chr20:13004000-13029200	Weak transcription	Ovary	ovary

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