Variant report

Variant	rs6126958
Chromosome Location	chr20:52411928-52411929
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52410629..52412192-chr20:55840697..55842515,2	MCF-7	breast:
2	chr20:50417725..50420436-chr20:52410501..52412991,2	MCF-7	breast:
3	chr20:52411903..52414095-chr20:52416977..52419626,3	K562	blood:
4	chr17:58469385..58471176-chr20:52411862..52414045,2	MCF-7	breast:
5	chr20:52410092..52412954-chr20:55842045..55843875,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170832	Chromatin interaction
ENSG00000225563	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000101115	Chromatin interaction
ENSG00000141371	Chromatin interaction
ENSG00000226308	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1117558	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1117559	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12625415	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4330164	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4361184	0.94[ASN][1000 genomes]
rs4416274	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4416275	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4618108	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4619669	0.94[ASN][1000 genomes]
rs56808127	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs58281268	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6123316	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6126956	0.81[AMR][1000 genomes]
rs6126962	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6126963	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6126964	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6126969	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6126970	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6126971	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6126972	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6126973	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62208437	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67468076	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv586221	chr20:52392390-52418987	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
6	nsv1064299	chr20:52395560-52420612	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
7	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
8	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:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52404200-52414400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr20:52404200-52415600	Weak transcription	Fetal Intestine Large	intestine
3	chr20:52406600-52417200	Weak transcription	K562	blood
4	chr20:52406800-52413600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr20:52408000-52413600	Weak transcription	A549	lung
6	chr20:52409400-52412200	Enhancers	Placenta	Placenta
7	chr20:52409400-52412600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr20:52409600-52412000	Enhancers	HMEC	breast
9	chr20:52409600-52412200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr20:52410600-52416400	Weak transcription	Liver	Liver
11	chr20:52411000-52412000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr20:52411000-52412000	Enhancers	Osteobl	bone
13	chr20:52411000-52415600	Weak transcription	Pancreas	Pancrea
14	chr20:52411200-52412000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr20:52411200-52412000	Enhancers	NHDF-Ad	bronchial
16	chr20:52411200-52412200	Enhancers	NH-A	brain
17	chr20:52411600-52412200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr20:52411600-52413600	Weak transcription	HepG2	liver
19	chr20:52411600-52415600	Weak transcription	Esophagus	oesophagus
20	chr20:52411600-52415600	Weak transcription	NHEK	skin
21	chr20:52411800-52415600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr20:52411800-52421400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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