Variant report

Variant	rs538789888
Chromosome Location	chr20:52556338-52556339
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:129)
CpG islands
(count:0)
Chromatin interactive
region (count:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:129 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr20:52556244-52556723	MCF10A-Er-Src	breast:	n/a	n/a
2	REST	chr20:52556191-52556941	A549	lung:	n/a	n/a
3	RAD21	chr20:52556315-52556838	HepG2	liver:	n/a	n/a
4	TCF12	chr20:52555870-52556981	SK-N-SH	brain:	n/a	n/a
5	TEAD4	chr20:52556183-52557141	K562	blood:	n/a	n/a
6	MAX	chr20:52555986-52556865	A549	lung:	n/a	n/a
7	ZC3H11A	chr20:52556199-52556902	K562	blood:	n/a	n/a
8	FOS	chr20:52556328-52556729	MCF10A-Er-Src	breast:	n/a	n/a
9	TBP	chr20:52556299-52556843	HepG2	liver:	n/a	n/a
10	CEBPB	chr20:52556052-52556884	A549	lung:	n/a	chr20:52556562-52556573
11	RUNX3	chr20:52556057-52556773	GM12878	blood:	n/a	n/a
12	GATA3	chr20:52556041-52556732	T-47D	breast:	n/a	n/a
13	FOXM1	chr20:52556259-52556977	GM12878	blood:	n/a	n/a
14	JUND	chr20:52556161-52556772	K562	blood:	n/a	n/a
15	RAD21	chr20:52556156-52556810	GM12878	blood:	n/a	n/a
16	GATA3	chr20:52556065-52556768	A549	lung:	n/a	n/a
17	EP300	chr20:52555969-52556912	A549	lung:	n/a	n/a
18	MAX	chr20:52555901-52556836	NB4	blood:	n/a	n/a
19	FOS	chr20:52556159-52556700	MCF10A-Er-Src	breast:	n/a	n/a
20	CEBPB	chr20:52555853-52556974	H1-hESC	embryonic stem cell:	n/a	chr20:52556562-52556573
21	RFX5	chr20:52556306-52556763	HepG2	liver:	n/a	n/a
22	BCLAF1	chr20:52556129-52556825	GM12878	blood:	n/a	n/a
23	NFIC	chr20:52555883-52556868	SK-N-SH	brain:	n/a	n/a
24	SMC3	chr20:52556200-52556878	GM12878	blood:	n/a	n/a
25	GATA3	chr20:52556082-52556734	T-47D	breast:	n/a	n/a
26	CHD1	chr20:52556314-52556792	GM12878	blood:	n/a	n/a
27	MAZ	chr20:52556212-52556766	HepG2	liver:	n/a	n/a
28	FOS	chr20:52556186-52556730	MCF10A-Er-Src	breast:	n/a	n/a
29	YY1	chr20:52556249-52557070	SK-N-SH	brain:	n/a	n/a
30	GATA3	chr20:52555861-52557022	A549	lung:	n/a	n/a
31	SMC3	chr20:52556201-52556823	HepG2	liver:	n/a	n/a
32	SMC3	chr20:52556337-52556831	K562	blood:	n/a	n/a
33	CTCF	chr20:52555655-52557361	SK-N-SH	brain:	n/a	n/a
34	PML	chr20:52556149-52557037	GM12878	blood:	n/a	n/a
35	CTCF	chr20:52556322-52556847	HepG2	liver:	n/a	n/a
36	RAD21	chr20:52556164-52556949	HCT-116	colon:	n/a	n/a
37	RCOR1	chr20:52556204-52556711	Hela-S3	cervix:	n/a	n/a
38	YY1	chr20:52556236-52557213	SK-N-SH	brain:	n/a	n/a
39	ATF2	chr20:52556289-52556872	GM12878	blood:	n/a	n/a
40	MAZ	chr20:52556260-52556831	K562	blood:	n/a	n/a
41	EP300	chr20:52556231-52556720	GM12878	blood:	n/a	n/a
42	CEBPB	chr20:52555843-52556814	K562	blood:	n/a	chr20:52556562-52556573
43	BCLAF1	chr20:52556036-52556925	GM12878	blood:	n/a	n/a
44	RAD21	chr20:52556145-52556757	SK-N-SH_RA	brain:	n/a	n/a
45	RAD21	chr20:52556206-52556898	H1-hESC	embryonic stem cell:	n/a	n/a
46	CEBPB	chr20:52555877-52556778	HepG2	liver:	n/a	chr20:52556562-52556573
47	FOXM1	chr20:52556299-52556912	GM12878	blood:	n/a	n/a
48	POLR2A	chr20:52556081-52556806	U87	brain:	n/a	n/a
49	RAD21	chr20:52556171-52557050	H1-hESC	embryonic stem cell:	n/a	n/a
50	STAT3	chr20:52556299-52556668	MCF10A-Er-Src	breast:	n/a	chr20:52556506-52556517

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52198633..52199695-chr20:52556115..52556780,3	MCF-7	breast:
2	chr20:52183255..52183876-chr20:52555683..52556411,2	MCF-7	breast:
3	chr17:59474996..59480161-chr20:52556121..52561884,6	MCF-7	breast:
4	chr1:147153898..147154477-chr20:52555683..52556390,2	MCF-7	breast:
5	chr20:52532023..52532688-chr20:52555703..52556632,2	MCF-7	breast:
6	chr20:49411382..49413304-chr20:52553862..52556702,3	MCF-7	breast:
7	chr17:58145680..58147362-chr20:52554822..52556632,2	MCF-7	breast:
8	chr20:52551745..52571491-chr20:55837843..55848700,39	MCF-7	breast:
9	chr17:56706658..56709234-chr20:52552890..52557689,4	MCF-7	breast:
10	chr17:59939253..59942212-chr20:52554185..52557076,2	MCF-7	breast:
11	chr20:52556025..52558052-chr4:57843937..57845567,2	MCF-7	breast:
12	chr17:59488616..59494924-chr20:52554630..52559372,9	MCF-7	breast:
13	chr20:52554429..52556366-chr20:55834185..55835777,2	MCF-7	breast:
14	chr20:52499798..52500636-chr20:52556044..52556576,2	MCF-7	breast:
15	chr20:52554988..52556740-chr20:55798732..55800489,2	MCF-7	breast:
16	chr12:81102346..81103912-chr20:52553556..52556381,2	MCF-7	breast:
17	chr17:56707751..56710392-chr20:52555190..52558925,4	MCF-7	breast:
18	chr20:52554098..52560340-chr20:52684210..52688448,9	MCF-7	breast:
19	chr20:49347041..49349298-chr20:52555192..52557887,2	MCF-7	breast:
20	chr17:59485646..59489353-chr20:52553682..52557868,4	MCF-7	breast:
21	chr20:52530757..52532897-chr20:52554790..52556353,2	K562	blood:
22	chr20:52556047..52557092-chr3:64008811..64009718,4	MCF-7	breast:
23	chr20:52554600..52557238-chr20:55797829..55800165,3	MCF-7	breast:
24	chr20:52553226..52558762-chr20:55837122..55843874,19	MCF-7	breast:
25	chr20:52224289..52226213-chr20:52555088..52557591,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000236352	TF binding region
ENSG00000121068	Chromatin interaction
ENSG00000265595	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000235415	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000084092	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000136492	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000064787	Chromatin interaction
ENSG00000124243	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000047315	Chromatin interaction
ENSG00000163636	Chromatin interaction
ENSG00000226308	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

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:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52549000-52558800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr20:52550000-52556800	Enhancers	Primary B cells from peripheral blood	blood
3	chr20:52550400-52557400	Enhancers	Placenta	Placenta
4	chr20:52551200-52556400	Weak transcription	Psoas Muscle	Psoas
5	chr20:52551800-52557000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr20:52552000-52556800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr20:52552000-52565200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr20:52552200-52557000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr20:52552200-52565400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr20:52552400-52566000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr20:52552600-52556400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr20:52552600-52556400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr20:52552600-52557400	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr20:52552600-52557800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr20:52552600-52564400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr20:52552800-52556600	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr20:52552800-52560200	Weak transcription	Primary T cells from cord blood	blood
18	chr20:52552800-52560200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr20:52553000-52556400	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr20:52553800-52556400	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr20:52553800-52558600	Enhancers	HepG2	liver
22	chr20:52554000-52557000	Weak transcription	Fetal Stomach	stomach
23	chr20:52554200-52559200	Enhancers	K562	blood
24	chr20:52554600-52560000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr20:52554600-52561000	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr20:52554800-52556400	Enhancers	HSMMtube	muscle
27	chr20:52554800-52565000	Weak transcription	Spleen	Spleen
28	chr20:52555000-52556400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr20:52555000-52557600	Enhancers	Colonic Mucosa	Colon
30	chr20:52555000-52557600	Enhancers	Stomach Mucosa	stomach
31	chr20:52555200-52556400	Weak transcription	Primary B cells from cord blood	blood
32	chr20:52555200-52556800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr20:52555200-52559400	Enhancers	Placenta Amnion	Placenta Amnion
34	chr20:52555400-52556600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr20:52555400-52556600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr20:52555400-52557000	Enhancers	HSMM	muscle
37	chr20:52555400-52557000	Enhancers	NHEK	skin
38	chr20:52555400-52557200	Enhancers	Brain Hippocampus Middle	brain
39	chr20:52555400-52557400	Enhancers	NHLF	lung
40	chr20:52555400-52557600	Enhancers	Brain Cingulate Gyrus	brain
41	chr20:52555400-52557600	Enhancers	Duodenum Mucosa	Duodenum
42	chr20:52555400-52557800	Enhancers	HMEC	breast
43	chr20:52555400-52559400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr20:52555400-52561000	Enhancers	Fetal Heart	heart
45	chr20:52555600-52556600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr20:52555600-52556800	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr20:52555600-52556800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr20:52555600-52556800	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr20:52555600-52556800	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr20:52555600-52556800	Enhancers	Stomach Smooth Muscle	stomach

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