Variant report

Variant	rs112253752
Chromosome Location	chr12:56400840-56400841
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:146)
CpG islands
(count:0)
Chromatin interactive
region (count:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:146 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP1	chr12:56400794-56401458	A549	lung:	n/a	chr12:56401236-56401250 chr12:56401435-56401444 chr12:56401434-56401448 chr12:56401240-56401249 chr12:56401433-56401445 chr12:56401239-56401251 chr12:56401392-56401402 chr12:56401434-56401443 chr12:56401433-56401445 chr12:56401434-56401444
2	POLR2A	chr12:56400770-56401248	U87	brain:	n/a	n/a
3	PML	chr12:56400623-56401443	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:56400602-56401375	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:56400693-56401280	K562	blood:	n/a	n/a
6	REST	chr12:56400809-56401399	A549	lung:	n/a	n/a
7	ATF2	chr12:56400778-56401316	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr12:56400662-56401467	ECC-1	luminal epithelium:	n/a	chr12:56401436-56401446
9	RCOR1	chr12:56400786-56401272	K562	blood:	n/a	n/a
10	GTF2F1	chr12:56400768-56401306	Hela-S3	cervix:	n/a	n/a
11	KAP1	chr12:56400746-56401152	HEK293	kidney:	n/a	n/a
12	POLR2A	chr12:56400683-56401569	ECC-1	luminal epithelium:	n/a	n/a
13	SRF	chr12:56400734-56401449	MCF-7	breast:	n/a	chr12:56401436-56401446
14	MAX	chr12:56400649-56401463	A549	lung:	n/a	chr12:56401436-56401446
15	FOXM1	chr12:56400789-56401405	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:56400686-56401483	ECC-1	luminal epithelium:	n/a	n/a
17	RFX5	chr12:56400773-56401355	Hela-S3	cervix:	n/a	n/a
18	NFATC1	chr12:56400824-56401243	GM12878	blood:	n/a	n/a
19	MAX	chr12:56400685-56401351	Hela-S3	cervix:	n/a	n/a
20	NFIC	chr12:56400793-56401257	HepG2	liver:	n/a	n/a
21	CBX3	chr12:56400621-56401340	K562	blood:	n/a	n/a
22	FOXM1	chr12:56400717-56401324	GM12878	blood:	n/a	n/a
23	HEY1	chr12:56400671-56401240	K562	blood:	n/a	n/a
24	POLR2A	chr12:56400796-56401449	HL-60	blood:	n/a	n/a
25	HCFC1	chr12:56400564-56401658	Hela-S3	cervix:	n/a	n/a
26	MYC	chr12:56400717-56401305	K562	blood:	n/a	n/a
27	MYBL2	chr12:56400604-56401393	HepG2	liver:	n/a	n/a
28	MXI1	chr12:56400836-56401229	K562	blood:	n/a	n/a
29	POLR2A	chr12:56400628-56401373	SK-N-SH	brain:	n/a	n/a
30	MAX	chr12:56400839-56401156	H1-hESC	embryonic stem cell:	n/a	n/a
31	TCF12	chr12:56400753-56402039	ECC-1	luminal epithelium:	n/a	n/a
32	POLR2A	chr12:56400540-56402452	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr12:56400723-56401220	HepG2	liver:	n/a	n/a
34	YY1	chr12:56400821-56401427	ECC-1	luminal epithelium:	n/a	chr12:56401324-56401338
35	POLR2A	chr12:56400580-56401379	GM12892	blood:	n/a	n/a
36	MAX	chr12:56400623-56401356	K562	blood:	n/a	n/a
37	NFATC1	chr12:56400782-56401299	GM12878	blood:	n/a	n/a
38	POLR2A	chr12:56400747-56401249	GM12892	blood:	n/a	n/a
39	POLR2A	chr12:56400720-56401533	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr12:56400696-56401400	PANC-1	pancreas:	n/a	n/a
41	MYBL2	chr12:56400612-56401420	HepG2	liver:	n/a	n/a
42	REST	chr12:56400758-56402521	H1-neurons	neurons:	n/a	chr12:56401778-56401791
43	POLR2A	chr12:56400637-56401330	K562	blood:	n/a	n/a
44	TBL1XR1	chr12:56400783-56401318	K562	blood:	n/a	n/a
45	POLR2A	chr12:56400615-56401329	HCT-116	colon:	n/a	n/a
46	POLR2A	chr12:56400719-56401392	K562	blood:	n/a	n/a
47	ZC3H11A	chr12:56400827-56401253	K562	blood:	n/a	n/a
48	TAF1	chr12:56400685-56402279	ECC-1	luminal epithelium:	n/a	n/a
49	SIX5	chr12:56400609-56401302	A549	lung:	n/a	n/a
50	MBD4	chr12:56400675-56401296	HepG2	liver:	n/a	n/a

No data

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

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	chr12:56221928..56223913-chr12:56399026..56401166,2	MCF-7	breast:
5	chr12:56364817..56368355-chr12:56399269..56402650,4	K562	blood:
6	chr12:56400102..56402586-chr12:56415416..56418384,2	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	chr12:56365318..56368355-chr12:56399244..56401399,3	K562	blood:
10	chr12:56388289..56393996-chr12:56394860..56404076,14	K562	blood:
11	chr12:56389364..56393818-chr12:56396293..56409099,19	MCF-7	breast:
12	chr12:56390656..56393336-chr12:56399432..56401234,2	K562	blood:
13	chr12:56399898..56405642-chr12:56433175..56438589,7	K562	blood:
14	chr12:56399617..56401195-chr12:56518712..56520569,2	K562	blood:
15	chr12:56399677..56401195-chr12:56518712..56520828,2	K562	blood:
16	chr12:56211633..56216017-chr12:56399885..56403410,4	MCF-7	breast:
17	chr12:56399605..56402732-chr12:56433705..56437280,6	MCF-7	breast:
18	chr12:56400079..56406275-chr12:56406695..56413732,8	MCF-7	breast:
19	chr12:56399990..56402705-chr12:56510349..56512541,3	K562	blood:
20	chr12:56399990..56401630-chr12:56510349..56512475,2	K562	blood:
21	chr12:56222087..56223926-chr12:56400815..56402785,2	MCF-7	breast:
22	chr12:56318939..56322802-chr12:56399424..56402892,5	MCF-7	breast:
23	chr12:56326233..56328752-chr12:56399282..56401795,2	MCF-7	breast:
24	chr12:56323623..56326295-chr12:56400061..56402642,2	MCF-7	breast:
25	chr12:56386715..56395273-chr12:56398367..56404356,15	MCF-7	breast:

No data

Variant related genes	Relation type
IKZF4	TF binding region
ENSG00000182796	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000258056	Chromatin interaction
ENSG00000258554	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000123374	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000139531	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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56400600-56401000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr12:56400600-56401000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:56400600-56401000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:56400600-56401000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:56400600-56401000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
6	chr12:56400600-56401000	Flanking Active TSS	Placenta	Placenta
7	chr12:56400600-56401000	Flanking Active TSS	Rectal Smooth Muscle	rectum
8	chr12:56400600-56401000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr12:56400600-56401000	Flanking Active TSS	Stomach Smooth Muscle	stomach
10	chr12:56400600-56401000	Flanking Active TSS	K562	blood
11	chr12:56400600-56401200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:56400600-56401200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:56400600-56401200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:56400600-56401200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:56400600-56401200	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr12:56400600-56401200	Flanking Active TSS	Brain Germinal Matrix	brain
17	chr12:56400600-56401200	Flanking Active TSS	Brain Hippocampus Middle	brain
18	chr12:56400600-56401200	Flanking Active TSS	Fetal Muscle Trunk	muscle
19	chr12:56400600-56401200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
20	chr12:56400600-56401200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr12:56400600-56401200	Flanking Active TSS	Stomach Mucosa	stomach
22	chr12:56400600-56401600	Active TSS	HMEC	breast
23	chr12:56400600-56401800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:56400600-56401800	Active TSS	Muscle Satellite Cultured Cells	--
25	chr12:56400600-56401800	Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr12:56400600-56401800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:56400600-56401800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:56400600-56401800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr12:56400600-56401800	Active TSS	Colonic Mucosa	Colon
30	chr12:56400600-56401800	Active TSS	Duodenum Mucosa	Duodenum
31	chr12:56400600-56401800	Active TSS	Esophagus	oesophagus
32	chr12:56400600-56401800	Active TSS	Fetal Brain Female	brain
33	chr12:56400600-56401800	Active TSS	Fetal Intestine Large	intestine
34	chr12:56400600-56401800	Active TSS	Fetal Intestine Small	intestine
35	chr12:56400600-56401800	Active TSS	Fetal Stomach	stomach
36	chr12:56400600-56401800	Active TSS	NH-A	brain
37	chr12:56400600-56401800	Active TSS	NHEK	skin
38	chr12:56400600-56402000	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr12:56400600-56402000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:56400600-56402000	Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr12:56400600-56402000	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr12:56400600-56402000	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr12:56400600-56402000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:56400600-56402000	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr12:56400600-56402000	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr12:56400600-56402000	Active TSS	Left Ventricle	heart
47	chr12:56400600-56402000	Active TSS	Pancreas	Pancrea
48	chr12:56400600-56402000	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr12:56400600-56402000	Active TSS	Right Ventricle	heart
50	chr12:56400600-56402000	Active TSS	NHDF-Ad	bronchial

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