Variant report

Variant	rs559703251
Chromosome Location	chr20:52556019-52556020
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr20:52555870-52556981	SK-N-SH	brain:	n/a	n/a
2	MAX	chr20:52555986-52556865	A549	lung:	n/a	n/a
3	EP300	chr20:52555969-52556912	A549	lung:	n/a	n/a
4	MAX	chr20:52555901-52556836	NB4	blood:	n/a	n/a
5	CEBPB	chr20:52555853-52556974	H1-hESC	embryonic stem cell:	n/a	chr20:52556562-52556573
6	NFIC	chr20:52555883-52556868	SK-N-SH	brain:	n/a	n/a
7	GATA3	chr20:52555861-52557022	A549	lung:	n/a	n/a
8	CTCF	chr20:52555655-52557361	SK-N-SH	brain:	n/a	n/a
9	CEBPB	chr20:52555843-52556814	K562	blood:	n/a	chr20:52556562-52556573
10	CEBPB	chr20:52555877-52556778	HepG2	liver:	n/a	chr20:52556562-52556573
11	EP300	chr20:52556018-52556916	A549	lung:	n/a	n/a
12	TEAD4	chr20:52554372-52558599	A549	lung:	n/a	n/a
13	MYC	chr20:52556001-52556787	MCF10A-Er-Src	breast:	n/a	n/a
14	BCL3	chr20:52555964-52556839	A549	lung:	n/a	n/a
15	POLR2A	chr20:52555970-52556335	GM12878	blood:	n/a	n/a
16	CTCF	chr20:52556000-52556150	HRPEpiC	eye:	n/a	n/a
17	MEF2A	chr20:52555814-52557004	SK-N-SH	brain:	n/a	n/a
18	PBX3	chr20:52555926-52556793	SK-N-SH	brain:	n/a	n/a
19	RAD21	chr20:52555770-52557145	SK-N-SH	brain:	n/a	n/a
20	MAX	chr20:52555887-52556953	A549	lung:	n/a	n/a
21	CEBPB	chr20:52555797-52556902	A549	lung:	n/a	chr20:52556562-52556573
22	GATA3	chr20:52555842-52556929	SK-N-SH	brain:	n/a	n/a
23	PBX3	chr20:52556016-52556803	SK-N-SH	brain:	n/a	n/a
24	TCF12	chr20:52555919-52556943	A549	lung:	n/a	n/a
25	CTCF	chr20:52555920-52556070	AG09319	gingival:	n/a	n/a
26	GATA3	chr20:52555873-52556914	SK-N-SH	brain:	n/a	n/a
27	SP1	chr20:52556019-52556819	A549	lung:	n/a	n/a
28	POLR2A	chr20:52555971-52556735	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr20:52555969-52556863	PANC-1	pancreas:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr20:52183255..52183876-chr20:52555683..52556411,2	MCF-7	breast:
2	chr1:147153898..147154477-chr20:52555683..52556390,2	MCF-7	breast:
3	chr20:52532023..52532688-chr20:52555703..52556632,2	MCF-7	breast:
4	chr20:52367473..52369879-chr20:52554123..52556023,3	K562	blood:
5	chr20:49411382..49413304-chr20:52553862..52556702,3	MCF-7	breast:
6	chr17:58145680..58147362-chr20:52554822..52556632,2	MCF-7	breast:
7	chr20:52551745..52571491-chr20:55837843..55848700,39	MCF-7	breast:
8	chr17:56706658..56709234-chr20:52552890..52557689,4	MCF-7	breast:
9	chr17:59939253..59942212-chr20:52554185..52557076,2	MCF-7	breast:
10	chr17:59488616..59494924-chr20:52554630..52559372,9	MCF-7	breast:
11	chr20:52554429..52556366-chr20:55834185..55835777,2	MCF-7	breast:
12	chr1:107819410..107820211-chr20:52555665..52556317,2	MCF-7	breast:
13	chr20:52554988..52556740-chr20:55798732..55800489,2	MCF-7	breast:
14	chr12:81102346..81103912-chr20:52553556..52556381,2	MCF-7	breast:
15	chr20:52553803..52556220-chr20:55831106..55834849,4	MCF-7	breast:
16	chr17:56707751..56710392-chr20:52555190..52558925,4	MCF-7	breast:
17	chr20:52554098..52560340-chr20:52684210..52688448,9	MCF-7	breast:
18	chr20:49347041..49349298-chr20:52555192..52557887,2	MCF-7	breast:
19	chr17:59485646..59489353-chr20:52553682..52557868,4	MCF-7	breast:
20	chr20:52552477..52556062-chr3:64098052..64101134,3	MCF-7	breast:
21	chr20:52530757..52532897-chr20:52554790..52556353,2	K562	blood:
22	chr20:52554600..52557238-chr20:55797829..55800165,3	MCF-7	breast:
23	chr20:52553226..52558762-chr20:55837122..55843874,19	MCF-7	breast:
24	chr20:52224289..52226213-chr20:52555088..52557591,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000236352	TF binding region
ENSG00000267280	Chromatin interaction
ENSG00000124243	Chromatin interaction
ENSG00000064787	Chromatin interaction
ENSG00000235415	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000265595	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000136492	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000124171	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:116 , 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	chr20:52551200-52556200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr20:52551200-52556400	Weak transcription	Psoas Muscle	Psoas
6	chr20:52551800-52556200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr20:52551800-52557000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr20:52552000-52556800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr20:52552000-52565200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr20:52552200-52556200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr20:52552200-52557000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr20:52552200-52565400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr20:52552400-52566000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr20:52552600-52556200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr20:52552600-52556200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr20:52552600-52556200	Weak transcription	Fetal Thymus	thymus
17	chr20:52552600-52556400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr20:52552600-52556400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr20:52552600-52557400	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr20:52552600-52557800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr20:52552600-52564400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr20:52552800-52556600	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr20:52552800-52560200	Weak transcription	Primary T cells from cord blood	blood
24	chr20:52552800-52560200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr20:52553000-52556200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr20:52553000-52556400	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr20:52553800-52556400	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr20:52553800-52558600	Enhancers	HepG2	liver
29	chr20:52554000-52557000	Weak transcription	Fetal Stomach	stomach
30	chr20:52554200-52556200	Weak transcription	Fetal Intestine Small	intestine
31	chr20:52554200-52559200	Enhancers	K562	blood
32	chr20:52554600-52560000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr20:52554600-52561000	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr20:52554800-52556400	Enhancers	HSMMtube	muscle
35	chr20:52554800-52565000	Weak transcription	Spleen	Spleen
36	chr20:52555000-52556400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr20:52555000-52557600	Enhancers	Colonic Mucosa	Colon
38	chr20:52555000-52557600	Enhancers	Stomach Mucosa	stomach
39	chr20:52555200-52556200	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr20:52555200-52556400	Weak transcription	Primary B cells from cord blood	blood
41	chr20:52555200-52556800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr20:52555200-52559400	Enhancers	Placenta Amnion	Placenta Amnion
43	chr20:52555400-52556200	Enhancers	Brain Anterior Caudate	brain
44	chr20:52555400-52556600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr20:52555400-52556600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr20:52555400-52557000	Enhancers	HSMM	muscle
47	chr20:52555400-52557000	Enhancers	NHEK	skin
48	chr20:52555400-52557200	Enhancers	Brain Hippocampus Middle	brain
49	chr20:52555400-52557400	Enhancers	NHLF	lung
50	chr20:52555400-52557600	Enhancers	Brain Cingulate Gyrus	brain

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