Variant report

Variant	rs6091793
Chromosome Location	chr20:52574739-52574740
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52559629..52560938-chr20:52573970..52574859,6	MCF-7	breast:
2	chr17:59914310..59915293-chr20:52574481..52574994,2	MCF-7	breast:
3	chr20:52572107..52575056-chr20:52680520..52683373,2	MCF-7	breast:
4	chr20:52560027..52561332-chr20:52573988..52574832,5	MCF-7	breast:
5	chr20:46483439..46484184-chr20:52574324..52575013,2	MCF-7	breast:
6	chr20:52573818..52574952-chr20:52679002..52679930,5	MCF-7	breast:
7	chr20:52573893..52576566-chr20:52684322..52688419,3	MCF-7	breast:
8	chr20:52573993..52574848-chr20:52673290..52674223,4	MCF-7	breast:
9	chr20:52557853..52560053-chr20:52573644..52576413,2	K562	blood:
10	chr20:52556172..52557026-chr20:52573973..52574991,4	MCF-7	breast:
11	chr17:56706951..56709239-chr20:52571954..52576924,4	MCF-7	breast:
12	chr17:56707924..56709444-chr20:52574671..52576672,2	MCF-7	breast:
13	chr20:52573998..52574858-chr3:64016096..64016874,2	MCF-7	breast:
14	chr20:52574055..52577130-chr20:55839672..55843479,4	MCF-7	breast:
15	chr2:197371996..197373539-chr20:52572973..52575210,2	MCF-7	breast:
16	chr20:52574355..52575313-chr20:53285096..53285689,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000236352	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000265595	Chromatin interaction
ENSG00000064787	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000212195	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1016279	0.93[CEU][hapmap];0.87[GIH][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10485440	0.86[TSI][hapmap]
rs10485441	0.87[CEU][hapmap]
rs1125895	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12480106	0.93[CEU][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1477639	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2024064	0.81[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2024066	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs208366	0.82[YRI][hapmap]
rs2108456	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2276494	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2276496	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2276497	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2276502	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2276510	0.83[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2302039	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35575210	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs371096	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3815270	1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs382133	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs402992	0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs4809946	0.84[JPT][hapmap]
rs4809947	0.84[JPT][hapmap]
rs55672258	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55776232	0.86[EUR][1000 genomes]
rs6022877	0.93[ASN][1000 genomes]
rs6091791	1.00[YRI][hapmap]
rs6091792	1.00[YRI][hapmap]
rs6091794	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6091796	1.00[YRI][hapmap]
rs6097694	1.00[YRI][hapmap]
rs6097696	1.00[YRI][hapmap]
rs6097716	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs714514	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7272317	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8124068	0.93[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs872923	0.94[JPT][hapmap]
rs872924	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
3	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
4	nsv1055549	chr20:52555871-52586281	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52564200-52576400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:52566400-52644800	Weak transcription	Gastric	stomach
3	chr20:52566600-52576200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr20:52566600-52576600	Weak transcription	Brain Anterior Caudate	brain
5	chr20:52566800-52576400	Weak transcription	Fetal Lung	lung
6	chr20:52567000-52576600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr20:52567000-52578200	Weak transcription	Brain Angular Gyrus	brain
8	chr20:52567000-52580200	Weak transcription	Stomach Mucosa	stomach
9	chr20:52570200-52591800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr20:52570200-52592400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr20:52570600-52576400	Weak transcription	Fetal Kidney	kidney
12	chr20:52570800-52590800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr20:52572400-52576200	Weak transcription	HepG2	liver
14	chr20:52572800-52575000	Enhancers	HSMMtube	muscle
15	chr20:52573400-52576200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr20:52573400-52576200	Enhancers	NHDF-Ad	bronchial
17	chr20:52573600-52575200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr20:52573600-52576200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr20:52573800-52574800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr20:52573800-52575000	Enhancers	NH-A	brain
21	chr20:52573800-52575200	Enhancers	Osteobl	bone
22	chr20:52574000-52574800	Enhancers	HSMM	muscle
23	chr20:52574000-52574800	Enhancers	NHLF	lung
24	chr20:52574000-52575600	Enhancers	Ovary	ovary
25	chr20:52574200-52577400	Enhancers	Fetal Stomach	stomach
26	chr20:52574400-52574800	Weak transcription	Brain Hippocampus Middle	brain
27	chr20:52574400-52574800	Enhancers	Brain Substantia Nigra	brain
28	chr20:52574600-52574800	Enhancers	H9 Cell Line	embryonic stem cell
29	chr20:52574600-52574800	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr20:52574600-52574800	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr20:52574600-52574800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr20:52574600-52575000	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr20:52574600-52576200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr20:52574600-52576200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr20:52574600-52576400	Enhancers	Adipose Nuclei	Adipose

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