Variant report

Variant	rs546707530
Chromosome Location	chr12:56401767-56401768
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr12:56401670-56402175	GM12878	blood:	n/a	n/a
2	MAX	chr12:56401587-56401894	K562	blood:	n/a	n/a
3	POLR2A	chr12:56401586-56402225	ECC-1	luminal epithelium:	n/a	n/a
4	EGR1	chr12:56401443-56401856	K562	blood:	n/a	chr12:56401549-56401563 chr12:56401570-56401584 chr12:56401614-56401628 chr12:56401496-56401505
5	TCF12	chr12:56400753-56402039	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr12:56400540-56402452	H1-hESC	embryonic stem cell:	n/a	n/a
7	HMGN3	chr12:56401636-56401824	K562	blood:	n/a	n/a
8	ZBTB7A	chr12:56401087-56401893	K562	blood:	n/a	chr12:56401271-56401285 chr12:56401270-56401284
9	MAX	chr12:56401521-56402058	ECC-1	luminal epithelium:	n/a	n/a
10	ZBTB7A	chr12:56400994-56402187	ECC-1	luminal epithelium:	n/a	chr12:56401271-56401285 chr12:56401270-56401284
11	REST	chr12:56400758-56402521	H1-neurons	neurons:	n/a	chr12:56401778-56401791
12	EGR1	chr12:56401361-56401865	K562	blood:	n/a	chr12:56401549-56401563 chr12:56401434-56401444 chr12:56401570-56401584 chr12:56401614-56401628 chr12:56401435-56401450 chr12:56401436-56401449 chr12:56401436-56401449 chr12:56401496-56401505
13	CHD1	chr12:56401718-56402099	H1-hESC	embryonic stem cell:	n/a	n/a
14	TAF1	chr12:56400685-56402279	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr12:56400647-56401957	K562	blood:	n/a	n/a
16	POLR2A	chr12:56400919-56401782	GM15510	blood:	n/a	n/a
17	POLR2A	chr12:56401553-56401874	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr12:56401582-56401849	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr12:56401599-56401898	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr12:56400985-56402134	H1-neurons	neurons:	n/a	n/a
21	TAF1	chr12:56401580-56402259	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr12:56400910-56401807	GM12892	blood:	n/a	n/a
23	POLR2A	chr12:56400840-56401931	H1-neurons	neurons:	n/a	n/a
24	POLR2A	chr12:56400804-56402240	H1-hESC	embryonic stem cell:	n/a	n/a
25	E2F6	chr12:56401606-56401902	K562	blood:	n/a	n/a
26	E2F6	chr12:56401689-56401908	K562	blood:	n/a	n/a
27	MAZ	chr12:56400871-56401889	K562	blood:	n/a	chr12:56401436-56401446
28	TBP	chr12:56401652-56401902	H1-hESC	embryonic stem cell:	n/a	n/a
29	ZBTB7A	chr12:56401029-56401898	K562	blood:	n/a	chr12:56401271-56401285 chr12:56401270-56401284
30	SP4	chr12:56401590-56401981	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr12:56400869-56401835	Raji	blood:	n/a	n/a
32	ZBTB7A	chr12:56400937-56402199	ECC-1	luminal epithelium:	n/a	chr12:56401271-56401285 chr12:56401270-56401284
33	E2F6	chr12:56401632-56402027	H1-hESC	embryonic stem cell:	n/a	n/a
34	ZBTB7A	chr12:56401538-56401896	HepG2	liver:	n/a	n/a
35	TAF1	chr12:56401585-56401937	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr12:56401554-56402063	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr12:56401385-56401971	SK-N-MC	brain:	n/a	n/a
38	POLR2A	chr12:56401561-56401930	H1-hESC	embryonic stem cell:	n/a	n/a
39	SIN3A	chr12:56401650-56402067	H1-hESC	embryonic stem cell:	n/a	n/a
40	MAZ	chr12:56400951-56401810	GM12878	blood:	n/a	chr12:56401436-56401446
41	POLR2A	chr12:56401531-56401943	GM12892	blood:	n/a	n/a
42	EGR1	chr12:56401455-56401890	ECC-1	luminal epithelium:	n/a	chr12:56401549-56401563 chr12:56401570-56401584 chr12:56401614-56401628 chr12:56401496-56401505
43	POLR2A	chr12:56401562-56402235	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr12:56400584-56402103	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56398950..56401873-chr12:56435306..56438317,7	MCF-7	breast:
2	chr12:56399175..56403137-chr12:56403716..56405667,4	MCF-7	breast:
3	chr12:56398217..56408038-chr12:56433794..56439966,15	K562	blood:
4	chr12:56364817..56368355-chr12:56399269..56402650,4	K562	blood:
5	chr12:56400102..56402586-chr12:56415416..56418384,2	MCF-7	breast:
6	chr12:56224367..56226323-chr12:56401356..56403743,2	MCF-7	breast:
7	chr12:56360672..56362289-chr12:56400535..56402399,2	MCF-7	breast:
8	chr12:56122770..56125786-chr12:56400050..56403264,3	K562	blood:
9	chr12:56400915..56403340-chr12:56510572..56513192,4	MCF-7	breast:
10	chr12:56388289..56393996-chr12:56394860..56404076,14	K562	blood:
11	chr12:56389364..56393818-chr12:56396293..56409099,19	MCF-7	breast:
12	chr12:56399898..56405642-chr12:56433175..56438589,7	K562	blood:
13	chr12:56211633..56216017-chr12:56399885..56403410,4	MCF-7	breast:
14	chr12:56399605..56402732-chr12:56433705..56437280,6	MCF-7	breast:
15	chr12:56390809..56392348-chr12:56401235..56403925,2	K562	blood:
16	chr12:56400079..56406275-chr12:56406695..56413732,8	MCF-7	breast:
17	chr12:56399990..56402705-chr12:56510349..56512541,3	K562	blood:
18	chr12:56401139..56403498-chr12:56475848..56478502,3	K562	blood:
19	chr12:56222087..56223926-chr12:56400815..56402785,2	MCF-7	breast:
20	chr12:56318939..56322802-chr12:56399424..56402892,5	MCF-7	breast:
21	chr12:56326233..56328752-chr12:56399282..56401795,2	MCF-7	breast:
22	chr12:56323623..56326295-chr12:56400061..56402642,2	MCF-7	breast:
23	chr12:56386715..56395273-chr12:56398367..56404356,15	MCF-7	breast:

Variant related genes	Relation type
IKZF4	TF binding region
ENSG00000139531	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000123374	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000258554	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000258056	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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	esv3444965	chr12:56400510-56402733	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	19 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	chr12:56400600-56401800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr12:56400600-56401800	Active TSS	Muscle Satellite Cultured Cells	--
3	chr12:56400600-56401800	Active TSS	Cortex derived primary cultured neurospheres	brain
4	chr12:56400600-56401800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:56400600-56401800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:56400600-56401800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:56400600-56401800	Active TSS	Colonic Mucosa	Colon
8	chr12:56400600-56401800	Active TSS	Duodenum Mucosa	Duodenum
9	chr12:56400600-56401800	Active TSS	Esophagus	oesophagus
10	chr12:56400600-56401800	Active TSS	Fetal Brain Female	brain
11	chr12:56400600-56401800	Active TSS	Fetal Intestine Large	intestine
12	chr12:56400600-56401800	Active TSS	Fetal Intestine Small	intestine
13	chr12:56400600-56401800	Active TSS	Fetal Stomach	stomach
14	chr12:56400600-56401800	Active TSS	NH-A	brain
15	chr12:56400600-56401800	Active TSS	NHEK	skin
16	chr12:56400600-56402000	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr12:56400600-56402000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:56400600-56402000	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr12:56400600-56402000	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr12:56400600-56402000	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr12:56400600-56402000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr12:56400600-56402000	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr12:56400600-56402000	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr12:56400600-56402000	Active TSS	Left Ventricle	heart
25	chr12:56400600-56402000	Active TSS	Pancreas	Pancrea
26	chr12:56400600-56402000	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr12:56400600-56402000	Active TSS	Right Ventricle	heart
28	chr12:56400600-56402000	Active TSS	NHDF-Ad	bronchial
29	chr12:56400600-56402000	Active TSS	NHLF	lung
30	chr12:56400600-56402200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr12:56400600-56402200	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr12:56400600-56402200	Active TSS	A549	lung
33	chr12:56400600-56402200	Active TSS	HSMM	muscle
34	chr12:56400600-56402400	Active TSS	H1 Cell Line	embryonic stem cell
35	chr12:56400600-56402400	Active TSS	H9 Cell Line	embryonic stem cell
36	chr12:56400600-56402400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:56400600-56402400	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr12:56400600-56402400	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr12:56400600-56402400	Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr12:56400600-56402400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:56400600-56402400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:56400600-56402400	Active TSS	Colon Smooth Muscle	Colon
43	chr12:56400600-56402400	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr12:56400800-56401800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:56400800-56401800	Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr12:56400800-56401800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr12:56400800-56401800	Active TSS	Gastric	stomach
48	chr12:56400800-56401800	Transcr. at gene 5' and 3'	Right Atrium	heart
49	chr12:56400800-56401800	Active TSS	Thymus	Thymus
50	chr12:56400800-56402000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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