Variant report

Variant	rs62208456
Chromosome Location	chr20:52424332-52424333
allele	G/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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:45987833..45989833-chr20:52422250..52425021,2	MCF-7	breast:
2	chr2:236462991..236465947-chr20:52423163..52425916,2	MCF-7	breast:
3	chr20:52423366..52426072-chr20:55815498..55818114,2	MCF-7	breast:
4	chr1:181069295..181072242-chr20:52423403..52424927,2	MCF-7	breast:
5	chr20:52423342..52425521-chr20:55839354..55842301,2	MCF-7	breast:
6	chr17:57914402..57919000-chr20:52421915..52427149,7	MCF-7	breast:
7	chr10:74855154..74857176-chr20:52422603..52424499,2	MCF-7	breast:
8	chr20:52406521..52409558-chr20:52424093..52427549,3	K562	blood:
9	chr20:52423838..52425788-chr8:37552737..37554558,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000062716	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000183779	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000122884	Chromatin interaction
ENSG00000101144	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11086441	0.82[AMR][1000 genomes]
rs2904374	0.81[AMR][1000 genomes]
rs4491782	0.86[AMR][1000 genomes]
rs4811471	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6126974	0.80[AMR][1000 genomes]
rs6126975	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv834008	chr20:52368660-52533410	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	185 gene(s)	inside rSNPs	diseases
3	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
4	nsv1057509	chr20:52390002-52431309	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
5	nsv1063442	chr20:52400519-52428220	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
6	nsv1060372	chr20:52409008-52502100	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	122 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52416000-52425600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr20:52418600-52430000	Weak transcription	Esophagus	oesophagus
3	chr20:52419600-52425600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr20:52422000-52425400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr20:52422000-52425800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr20:52422200-52425800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr20:52422200-52425800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr20:52422200-52425800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr20:52422600-52431400	Weak transcription	HepG2	liver
10	chr20:52423600-52432400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr20:52423800-52425600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr20:52423800-52425600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr20:52423800-52425800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr20:52423800-52425800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr20:52423800-52425800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr20:52423800-52425800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr20:52423800-52425800	Weak transcription	NHEK	skin
18	chr20:52423800-52426000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr20:52423800-52430400	Weak transcription	NHDF-Ad	bronchial
20	chr20:52423800-52436200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr20:52424000-52425400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr20:52424000-52425400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr20:52424000-52425600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr20:52424000-52425600	Weak transcription	A549	lung

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