Variant report

Variant	rs564159193
Chromosome Location	chr3:48956846-48956847
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:159)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:159 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD2	chr3:48955684-48956913	Hela-S3	cervix:	n/a	n/a
2	CTCF	chr3:48956840-48956990	HBMEC	blood vessel:	n/a	n/a
3	POLR2A	chr3:48955622-48957513	K562	blood:	n/a	n/a
4	CHD1	chr3:48955533-48957765	IMR90	lung:	n/a	n/a
5	UBTF	chr3:48955649-48957078	K562	blood:	n/a	n/a
6	CTCF	chr3:48956780-48956930	GM12874	blood:	n/a	n/a
7	POLR2A	chr3:48955883-48956909	HEK293	kidney:	n/a	n/a
8	HCFC1	chr3:48955446-48957694	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr3:48955591-48957632	HUVEC	blood vessel:	n/a	n/a
10	GABPA	chr3:48955704-48956868	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr3:48955395-48957740	GM12878	blood:	n/a	n/a
12	CTCF	chr3:48956720-48956870	Hela-S3	cervix:	n/a	n/a
13	MXI1	chr3:48955627-48957576	HepG2	liver:	n/a	n/a
14	SIN3AK20	chr3:48955824-48957037	PANC-1	pancreas:	n/a	n/a
15	MAX	chr3:48955523-48957237	SK-N-SH	brain:	n/a	n/a
16	BCLAF1	chr3:48955541-48957098	GM12878	blood:	n/a	chr3:48956860-48956873 chr3:48956720-48956729
17	GATA1	chr3:48955593-48957469	PBDE	blood:	n/a	n/a
18	CTCF	chr3:48956700-48956850	AG04449	skin:	n/a	n/a
19	MAX	chr3:48955611-48957523	GM12878	blood:	n/a	chr3:48957381-48957391
20	MAX	chr3:48956246-48957446	A549	lung:	n/a	chr3:48957381-48957391
21	SIN3AK20	chr3:48956827-48957122	H1-hESC	embryonic stem cell:	n/a	n/a
22	USF1	chr3:48956763-48957655	HCT-116	colon:	n/a	chr3:48957380-48957391
23	POLR2A	chr3:48955558-48957494	Hela-S3	cervix:	n/a	n/a
24	NR2F2	chr3:48955904-48956978	MCF-7	breast:	n/a	chr3:48956651-48956666
25	POLR2A	chr3:48955479-48957684	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr3:48955456-48956943	GM12891	blood:	n/a	n/a
27	POLR2A	chr3:48955549-48956905	GM19099	blood:	n/a	n/a
28	POLR2A	chr3:48955738-48957113	PFSK-1	brain:	n/a	n/a
29	YY1	chr3:48956711-48957107	GM12878	blood:	n/a	chr3:48956861-48956875
30	PML	chr3:48955461-48957615	GM12878	blood:	n/a	n/a
31	BACH1	chr3:48956765-48956949	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr3:48955584-48956957	GM18951	blood:	n/a	n/a
33	POLR2A	chr3:48956652-48957585	GM12892	blood:	n/a	n/a
34	MAX	chr3:48955575-48957609	K562	blood:	n/a	chr3:48957381-48957391
35	MAX	chr3:48955477-48957761	HepG2	liver:	n/a	chr3:48957381-48957391
36	E2F1	chr3:48956008-48956955	Hela-S3	cervix:	n/a	chr3:48956839-48956854 chr3:48956684-48956694 chr3:48956628-48956640
37	CTCF	chr3:48956720-48956870	GM12872	blood:	n/a	n/a
38	SMC3	chr3:48956605-48957505	Hela-S3	cervix:	n/a	n/a
39	MXI1	chr3:48955445-48957924	SK-N-SH	brain:	n/a	n/a
40	CTCF	chr3:48956700-48956850	GM12871	blood:	n/a	n/a
41	MAZ	chr3:48955615-48957138	IMR90	lung:	n/a	n/a
42	POLR2A	chr3:48956812-48957574	GM12891	blood:	n/a	n/a
43	POLR2A	chr3:48955525-48956936	GM12878	blood:	n/a	n/a
44	RUNX3	chr3:48955446-48956888	GM12878	blood:	n/a	n/a
45	CHD1	chr3:48956816-48957387	H1-hESC	embryonic stem cell:	n/a	n/a
46	STAT5A	chr3:48955413-48957404	GM12878	blood:	n/a	n/a
47	POLR2A	chr3:48955567-48957079	Hela-S3	cervix:	n/a	n/a
48	MXI1	chr3:48955641-48957668	Hela-S3	cervix:	n/a	n/a
49	ELF1	chr3:48955708-48956898	GM12878	blood:	n/a	chr3:48956859-48956871 chr3:48956267-48956280 chr3:48956238-48956251
50	GABPA	chr3:48955627-48956951	A549	lung:	n/a	n/a

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48955974..48957797-chr3:49448912..49450941,2	K562	blood:
2	chr3:48956178..48958930-chr3:48964681..48967359,2	MCF-7	breast:
3	chr3:48722838..48724823-chr3:48955919..48958463,2	K562	blood:
4	chr3:48753119..48755656-chr3:48955067..48957607,2	MCF-7	breast:
5	chr3:48955220..48957658-chr3:48960315..48963071,3	MCF-7	breast:
6	chr3:48954426..48959569-chr3:49057203..49060067,5	K562	blood:
7	chr3:48700103..48702620-chr3:48955233..48957367,3	K562	blood:
8	chr3:48700863..48702620-chr3:48955867..48958209,2	K562	blood:
9	chr3:48954616..48957728-chr3:49043769..49045935,3	K562	blood:
10	chr3:48956190..48958160-chr3:48963848..48966266,2	MCF-7	breast:
11	chr10:1034212..1034872-chr3:48956219..48957108,3	Hela-S3	cervix:
12	chr3:48934472..48936493-chr3:48955282..48957052,2	MCF-7	breast:
13	chr3:48777544..48781186-chr3:48954650..48958375,5	K562	blood:
14	chr19:2051176..2051694-chr3:48956146..48956931,2	Hela-S3	cervix:
15	chr3:48955694..48958185-chr3:49021057..49023573,2	K562	blood:
16	chr3:48882526..48886164-chr3:48952991..48958735,8	K562	blood:
17	chr3:48882526..48887589-chr3:48952932..48958567,11	K562	blood:
18	chr19:36544745..36545679-chr3:48956268..48957255,2	Hela-S3	cervix:
19	chr16:685835..686394-chr3:48956427..48956935,2	Hela-S3	cervix:
20	chr3:48956092..48958804-chr3:49057398..49059224,2	K562	blood:
21	chr3:48777662..48781214-chr3:48954479..48957215,3	K562	blood:
22	chr3:48933374..48937590-chr3:48954193..48958596,7	K562	blood:

No data

Variant related genes	Relation type
ARIH2OS	TF binding region
ARIH2	TF binding region
ENSG00000273211	Chromatin interaction
ENSG00000008300	Chromatin interaction
ENSG00000199032	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000178537	Chromatin interaction
ENSG00000099875	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000178252	Chromatin interaction
ENSG00000145022	Chromatin interaction
ENSG00000068745	Chromatin interaction
ENSG00000228350	Chromatin interaction
ENSG00000130731	Chromatin interaction
ENSG00000205740	Chromatin interaction
ENSG00000177479	Chromatin interaction
ENSG00000114302	Chromatin interaction
ENSG00000224424	Chromatin interaction
ENSG00000235236	Chromatin interaction
ENSG00000213672	Chromatin interaction
ENSG00000107937	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000161277	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487342	chr3:48823957-48960475	Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	esv3487343	chr3:48823963-48960381	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv980012	chr3:48935037-48963512	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	esv3394753	chr3:48956248-48960046	Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	esv3340246	chr3:48956448-48960646	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48954800-48957200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:48954800-48957200	Active TSS	Rectal Smooth Muscle	rectum
3	chr3:48954800-48957800	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr3:48955000-48957000	Active TSS	Primary T cells from cord blood	blood
5	chr3:48955000-48957600	Active TSS	Fetal Brain Female	brain
6	chr3:48955000-48957600	Active TSS	HSMM	muscle
7	chr3:48955200-48957000	Active TSS	Duodenum Mucosa	Duodenum
8	chr3:48955200-48957200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:48955200-48957200	Active TSS	Brain Cingulate Gyrus	brain
10	chr3:48955200-48957600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:48955200-48957600	Active TSS	Fetal Intestine Small	intestine
12	chr3:48955200-48957600	Active TSS	Hela-S3	cervix
13	chr3:48955200-48957800	Active TSS	Colonic Mucosa	Colon
14	chr3:48955200-48957800	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr3:48955200-48957800	Active TSS	Rectal Mucosa Donor 31	rectum
16	chr3:48955200-48958200	Active TSS	GM12878-XiMat	blood
17	chr3:48955200-48958200	Active TSS	K562	blood
18	chr3:48955400-48957000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:48955400-48957000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:48955400-48957200	Active TSS	H1 Cell Line	embryonic stem cell
21	chr3:48955400-48957200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:48955400-48957200	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr3:48955400-48957200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:48955400-48957200	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr3:48955400-48957200	Active TSS	Brain Angular Gyrus	brain
26	chr3:48955400-48957200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:48955400-48957200	Active TSS	Brain Substantia Nigra	brain
28	chr3:48955400-48957200	Active TSS	Fetal Kidney	kidney
29	chr3:48955400-48957200	Active TSS	Fetal Stomach	stomach
30	chr3:48955400-48957200	Active TSS	Thymus	Thymus
31	chr3:48955400-48957400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:48955400-48957400	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr3:48955400-48957400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:48955400-48957400	Active TSS	Colon Smooth Muscle	Colon
35	chr3:48955400-48957400	Active TSS	Esophagus	oesophagus
36	chr3:48955400-48957400	Active TSS	Left Ventricle	heart
37	chr3:48955400-48957600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:48955400-48957600	Active TSS	Pancreas	Pancrea
39	chr3:48955400-48957600	Active TSS	HSMMtube	muscle
40	chr3:48955400-48957800	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr3:48955400-48957800	Active TSS	H9 Cell Line	embryonic stem cell
42	chr3:48955400-48957800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:48955400-48957800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:48955400-48957800	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr3:48955400-48957800	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr3:48955400-48957800	Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr3:48955400-48957800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:48955400-48957800	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr3:48955400-48957800	Active TSS	Psoas Muscle	Psoas
50	chr3:48955400-48957800	Active TSS	Right Atrium	heart

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