Variant report

Variant	rs6097693
Chromosome Location	chr20:52576493-52576494
allele	A/C
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52576003..52577529-chr20:52812898..52814510,2	MCF-7	breast:
2	chr20:52573893..52576566-chr20:52684322..52688419,3	MCF-7	breast:
3	chr20:52575166..52577110-chr20:52817182..52819499,2	MCF-7	breast:
4	chr17:56706951..56709239-chr20:52571954..52576924,4	MCF-7	breast:
5	chr1:201118101..201120636-chr20:52576111..52577980,2	MCF-7	breast:
6	chr17:56735101..56737749-chr20:52575346..52577054,2	MCF-7	breast:
7	chr12:120729283..120731029-chr20:52576003..52578392,2	MCF-7	breast:
8	chr17:56707924..56709444-chr20:52574671..52576672,2	MCF-7	breast:
9	chr17:59947480..59950450-chr20:52574915..52576530,2	MCF-7	breast:
10	chr20:52574055..52577130-chr20:55839672..55843479,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000064787	Chromatin interaction
ENSG00000265595	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000101144	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1034843	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs158544	1.00[EUR][1000 genomes]
rs208364	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs208372	1.00[EUR][1000 genomes]
rs208373	1.00[EUR][1000 genomes]
rs208375	1.00[EUR][1000 genomes]
rs2276492	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2276508	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2276511	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276512	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299727	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2299733	0.93[ASN][1000 genomes]
rs2299736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290389	1.00[EUR][1000 genomes]
rs36030456	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs406691	0.95[ASN][1000 genomes]
rs4809948	0.93[ASN][1000 genomes]
rs4811488	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6091791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6091792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6091796	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6091799	0.95[ASN][1000 genomes]
rs6097694	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6097695	0.95[ASN][1000 genomes]
rs6097696	0.92[ASN][1000 genomes]
rs6097697	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]

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:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52566400-52644800	Weak transcription	Gastric	stomach
2	chr20:52566600-52576600	Weak transcription	Brain Anterior Caudate	brain
3	chr20:52567000-52576600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr20:52567000-52578200	Weak transcription	Brain Angular Gyrus	brain
5	chr20:52567000-52580200	Weak transcription	Stomach Mucosa	stomach
6	chr20:52570200-52591800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr20:52570200-52592400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr20:52570800-52590800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr20:52574200-52577400	Enhancers	Fetal Stomach	stomach
10	chr20:52574800-52578200	Weak transcription	Brain Substantia Nigra	brain
11	chr20:52575200-52576600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr20:52575600-52578400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr20:52576200-52576800	Flanking Active TSS	NHDF-Ad	bronchial
14	chr20:52576200-52577000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr20:52576200-52577000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr20:52576200-52577000	Flanking Active TSS	Osteobl	bone
17	chr20:52576200-52577200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr20:52576200-52577400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr20:52576200-52577400	Enhancers	Muscle Satellite Cultured Cells	--
20	chr20:52576200-52577800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr20:52576400-52576800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr20:52576400-52576800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr20:52576400-52576800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr20:52576400-52576800	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr20:52576400-52576800	Enhancers	Placenta	Placenta
26	chr20:52576400-52576800	Active TSS	Stomach Smooth Muscle	stomach
27	chr20:52576400-52576800	Flanking Active TSS	HepG2	liver
28	chr20:52576400-52577000	Enhancers	H9 Cell Line	embryonic stem cell
29	chr20:52576400-52577000	Enhancers	Fetal Muscle Leg	muscle
30	chr20:52576400-52577000	Enhancers	NHLF	lung
31	chr20:52576400-52577200	Enhancers	HSMMtube	muscle
32	chr20:52576400-52577400	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr20:52576400-52577400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr20:52576400-52577400	Enhancers	NH-A	brain
35	chr20:52576400-52577600	Enhancers	Fetal Lung	lung
36	chr20:52576400-52577800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr20:52576400-52578200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr20:52576400-52578200	Enhancers	Fetal Kidney	kidney
39	chr20:52576400-52578400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr20:52576400-52578400	Enhancers	HSMM	muscle
41	chr20:52576400-52578600	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr20:52576400-52578600	Enhancers	Brain Hippocampus Middle	brain
43	chr20:52576400-52591400	Weak transcription	Rectal Mucosa Donor 29	rectum

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