Variant report

Variant	rs6041777
Chromosome Location	chr20:13011475-13011476
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:13010524..13012462-chr20:13019943..13021816,2	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]
rs1549824	0.98[EUR][1000 genomes]
rs16993653	0.82[GIH][hapmap]
rs16993660	0.89[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs171499	0.96[EUR][1000 genomes]
rs17226299	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes]
rs17226306	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs17226313	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17812078	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17812085	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes]
rs17812091	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes]
rs17812097	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs3848768	0.88[CEU][hapmap];0.86[GIH][hapmap];0.82[EUR][1000 genomes]
rs4555414	0.96[EUR][1000 genomes]
rs56022742	0.94[EUR][1000 genomes]
rs6033569	0.94[EUR][1000 genomes]
rs6033573	0.86[CEU][hapmap];0.98[EUR][1000 genomes]
rs6033575	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6033592	0.84[EUR][1000 genomes]
rs6041760	0.94[EUR][1000 genomes]
rs6041766	0.98[EUR][1000 genomes]
rs6041768	0.89[CEU][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes]
rs6041776	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6041791	0.82[GIH][hapmap]
rs6109665	0.89[CEU][hapmap];0.98[EUR][1000 genomes]
rs673694	0.92[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:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13003400-13015400	Weak transcription	Duodenum Mucosa	Duodenum
2	chr20:13003800-13014600	Weak transcription	Esophagus	oesophagus
3	chr20:13003800-13026400	Weak transcription	Aorta	Aorta
4	chr20:13003800-13049600	Weak transcription	Lung	lung
5	chr20:13004000-13013000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr20:13004000-13027200	Weak transcription	Pancreas	Pancrea
7	chr20:13004000-13029200	Weak transcription	Ovary	ovary
8	chr20:13005400-13012800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr20:13006600-13014000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr20:13007400-13011800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr20:13007400-13012000	Enhancers	HSMM	muscle
12	chr20:13007600-13011600	Enhancers	HSMMtube	muscle
13	chr20:13007800-13012400	Enhancers	Placenta Amnion	Placenta Amnion
14	chr20:13007800-13014200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr20:13007800-13016200	Weak transcription	Left Ventricle	heart
16	chr20:13008000-13011800	Enhancers	Muscle Satellite Cultured Cells	--
17	chr20:13008400-13013000	Weak transcription	Liver	Liver
18	chr20:13008400-13014600	Genic enhancers	Placenta	Placenta
19	chr20:13008600-13011600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr20:13008600-13011600	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr20:13008600-13011600	Enhancers	NH-A	brain
22	chr20:13009200-13011600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr20:13009400-13011600	Enhancers	NHDF-Ad	bronchial
24	chr20:13009400-13012000	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr20:13009600-13015800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr20:13010000-13011600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr20:13010800-13012600	Enhancers	NHEK	skin
28	chr20:13011000-13013400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr20:13011000-13022600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr20:13011200-13011600	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr20:13011200-13011600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr20:13011200-13011800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr20:13011200-13011800	Enhancers	Osteobl	bone
34	chr20:13011200-13012200	Weak transcription	Fetal Intestine Large	intestine
35	chr20:13011200-13012600	Enhancers	HMEC	breast
36	chr20:13011200-13012800	Weak transcription	Fetal Intestine Small	intestine
37	chr20:13011200-13018800	Strong transcription	HepG2	liver
38	chr20:13011400-13011800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr20:13011400-13011800	Enhancers	A549	lung
40	chr20:13011400-13016800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr20:13011400-13026800	Weak transcription	Stomach Mucosa	stomach

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