Variant report

Variant	rs6078890
Chromosome Location	chr20:13003255-13003256
allele	A/G
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: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11698429	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12479968	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12481402	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17190775	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17190782	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2327446	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3761894	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3761896	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3843767	0.85[EUR][1000 genomes]
rs3859619	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4813104	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55646676	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58975911	0.90[ASN][1000 genomes]
rs6033574	0.80[ASN][1000 genomes]
rs6074543	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6074544	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6074545	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6078872	0.85[EUR][1000 genomes]
rs6078875	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6078877	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6078886	0.88[ASN][1000 genomes]
rs6078887	0.88[ASN][1000 genomes]
rs6078889	0.90[ASN][1000 genomes]
rs6078891	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6078895	0.86[AMR][1000 genomes];0.90[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:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:12991200-13003600	Weak transcription	Pancreas	Pancrea
2	chr20:12997600-13003800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr20:12997800-13008200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr20:13000800-13003400	ZNF genes & repeats	NHEK	skin
5	chr20:13001400-13003400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
6	chr20:13001400-13003800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr20:13001600-13003400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
8	chr20:13001600-13003400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr20:13001600-13004000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr20:13002200-13003400	ZNF genes & repeats	Thymus	Thymus
11	chr20:13002200-13003800	ZNF genes & repeats	Aorta	Aorta
12	chr20:13002200-13004200	Strong transcription	Fetal Intestine Large	intestine
13	chr20:13002600-13003600	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
14	chr20:13002600-13003600	ZNF genes & repeats	Fetal Intestine Small	intestine
15	chr20:13002600-13003800	Genic enhancers	Placenta	Placenta
16	chr20:13002800-13003800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr20:13002800-13004000	Enhancers	Muscle Satellite Cultured Cells	--
18	chr20:13003000-13003600	Enhancers	Placenta Amnion	Placenta Amnion
19	chr20:13003000-13003600	Genic enhancers	HepG2	liver
20	chr20:13003000-13003800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr20:13003000-13003800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr20:13003000-13003800	Strong transcription	Liver	Liver
23	chr20:13003000-13003800	Enhancers	Left Ventricle	heart
24	chr20:13003000-13003800	Enhancers	HUVEC	blood vessel
25	chr20:13003000-13003800	Enhancers	NH-A	brain
26	chr20:13003000-13004000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr20:13003000-13004000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr20:13003000-13004000	Enhancers	Right Atrium	heart
29	chr20:13003000-13004000	Enhancers	HMEC	breast
30	chr20:13003000-13004000	Enhancers	HSMM	muscle
31	chr20:13003000-13004000	Enhancers	Osteobl	bone
32	chr20:13003000-13004200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr20:13003000-13006000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr20:13003200-13003800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr20:13003200-13004000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr20:13003200-13004000	Strong transcription	Ovary	ovary
37	chr20:13003200-13004000	Enhancers	NHDF-Ad	bronchial
38	chr20:13003200-13004000	Enhancers	NHLF	lung

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