Variant report

Variant	rs6097779
Chromosome Location	chr20:52750059-52750060
allele	A/G
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:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:57922783..57925093-chr20:52747616..52750440,2	MCF-7	breast:
2	chr17:57913131..57926939-chr20:52735776..52751538,42	MCF-7	breast:
3	chr20:52732059..52732575-chr20:52749314..52750086,2	MCF-7	breast:
4	chr20:46640095..46644047-chr20:52746837..52750756,3	MCF-7	breast:
5	chr20:46413224..46418685-chr20:52746491..52752686,10	MCF-7	breast:
6	chr12:52636521..52638723-chr20:52748359..52750383,2	MCF-7	breast:
7	chr12:53344317..53347285-chr20:52748753..52751041,2	MCF-7	breast:
8	chr20:52749844..52752672-chrX:76227808..76229967,2	MCF-7	breast:
9	chr20:52748698..52751291-chr5:43063719..43066495,2	MCF-7	breast:
10	chr20:52749860..52752197-chr8:108092484..108095332,2	MCF-7	breast:
11	chr17:56735202..56737939-chr20:52748696..52751920,4	MCF-7	breast:
12	chr20:52749967..52752847-chr20:52755293..52758111,2	K562	blood:
13	chr17:56736366..56738088-chr20:52748194..52751006,3	MCF-7	breast:
14	chr20:46417525..46420204-chr20:52747771..52750602,2	MCF-7	breast:
15	chr20:52720225..52723216-chr20:52749431..52752183,2	K562	blood:
16	chr20:52749888..52750589-chr20:52813974..52814709,2	MCF-7	breast:
17	chr20:46616780..46618691-chr20:52748141..52750829,2	MCF-7	breast:
18	chr17:56707619..56710651-chr20:52747363..52752620,6	MCF-7	breast:
19	chr17:56704127..56711907-chr20:52729106..52752952,70	MCF-7	breast:
20	chr20:52749818..52752750-chr5:43554749..43557451,2	MCF-7	breast:
21	chr15:63794674..63797406-chr20:52748938..52750854,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000237423	Chromatin interaction
ENSG00000225410	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000265039	Chromatin interaction
ENSG00000135480	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000140455	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000172239	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000196562	Chromatin interaction
ENSG00000111057	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12624824	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2045844	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6022979	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6068799	0.82[MEX][hapmap]
rs6068802	0.82[MEX][hapmap]
rs6091821	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6091822	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6097777	0.89[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.84[TSI][hapmap];0.96[ASN][1000 genomes]
rs6097789	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6097795	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6097809	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6123360	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6127107	0.82[MEX][hapmap]
rs6127114	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62214478	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62214479	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62214503	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8117026	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8120563	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8124440	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8124792	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv586280	chr20:52718555-52758416	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	84 gene(s)	inside rSNPs	diseases
3	nsv912945	chr20:52746724-52772741	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52748000-52750400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr20:52748200-52750200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr20:52748200-52750200	Enhancers	Placenta	Placenta
4	chr20:52748200-52750400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr20:52748200-52751800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr20:52748200-52751800	Enhancers	HMEC	breast
7	chr20:52748400-52750600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr20:52748400-52750600	Flanking Active TSS	HepG2	liver
9	chr20:52748400-52750800	Enhancers	Placenta Amnion	Placenta Amnion
10	chr20:52748400-52751400	Enhancers	NHLF	lung
11	chr20:52748800-52750400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr20:52748800-52751000	Flanking Active TSS	A549	lung
13	chr20:52748800-52751600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr20:52749000-52750200	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr20:52749200-52750200	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr20:52749200-52750200	Enhancers	Fetal Muscle Leg	muscle
17	chr20:52749400-52750200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr20:52749400-52750200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr20:52749400-52750400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr20:52749400-52751400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr20:52749400-52751600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr20:52749400-52751800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr20:52749600-52750200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr20:52749600-52750200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr20:52749600-52750200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr20:52749600-52750200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr20:52749600-52750200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr20:52749600-52750200	Flanking Active TSS	Hela-S3	cervix
29	chr20:52749600-52750400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr20:52749600-52750400	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr20:52749600-52750400	Flanking Active TSS	NHDF-Ad	bronchial
32	chr20:52749600-52750400	Flanking Active TSS	Osteobl	bone
33	chr20:52749600-52750600	Enhancers	Brain Hippocampus Middle	brain
34	chr20:52749800-52750200	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr20:52749800-52750200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr20:52749800-52750200	Active TSS	Brain Cingulate Gyrus	brain
37	chr20:52749800-52750200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
38	chr20:52749800-52750200	Flanking Active TSS	HSMM	muscle
39	chr20:52749800-52750400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr20:52749800-52750400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr20:52750000-52750200	Enhancers	Left Ventricle	heart
42	chr20:52750000-52750200	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr20:52750000-52750200	Flanking Active TSS	NH-A	brain
44	chr20:52750000-52750200	Flanking Active TSS	NHEK	skin
45	chr20:52750000-52750400	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr20:52750000-52750400	Enhancers	Brain Substantia Nigra	brain
47	chr20:52750000-52750400	Enhancers	HSMMtube	muscle
48	chr20:52750000-52750400	Enhancers	Monocytes-CD14+_RO01746	blood

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