Variant report

Variant	rs3759303
Chromosome Location	chr12:106643004-106643005
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:106641572-106644424	GM12891	blood:	n/a	n/a
2	POLR2A	chr12:106642680-106643257	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr12:106640579-106644067	GM19193	blood:	n/a	n/a
4	RCOR1	chr12:106642831-106643053	HepG2	liver:	n/a	n/a
5	FOXA2	chr12:106642962-106643380	A549	lung:	n/a	n/a
6	STAT3	chr12:106642719-106643018	MCF10A-Er-Src	breast:	n/a	n/a
7	SIN3A	chr12:106641582-106643087	H1-hESC	embryonic stem cell:	n/a	chr12:106641703-106641716 chr12:106641733-106641742
8	MTA3	chr12:106642867-106643431	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:106641025-106644169	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:106641115-106643709	MCF10A-Er-Src	breast:	n/a	n/a
11	CHD1	chr12:106639633-106643296	IMR90	lung:	n/a	chr12:106641025-106641035
12	POLR2A	chr12:106641063-106643175	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr12:106641448-106643261	HUVEC	blood vessel:	n/a	n/a
14	FOS	chr12:106642785-106643048	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr12:106640869-106644014	GM18951	blood:	n/a	n/a
16	RELA	chr12:106642205-106643879	GM15510	blood:	n/a	n/a
17	CEBPB	chr12:106642837-106643208	IMR90	lung:	n/a	n/a
18	POLR2A	chr12:106639680-106643402	IMR90	lung:	n/a	n/a
19	MAZ	chr12:106639576-106643317	IMR90	lung:	n/a	chr12:106641917-106641927
20	POLR2A	chr12:106641586-106643325	HepG2	liver:	n/a	n/a
21	FOXA1	chr12:106642965-106643337	HepG2	liver:	n/a	n/a
22	POLR2A	chr12:106642213-106643167	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr12:106640930-106644009	GM12892	blood:	n/a	n/a
24	STAT3	chr12:106642407-106643133	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr12:106640929-106644016	GM15510	blood:	n/a	n/a
26	FOS	chr12:106642653-106643078	MCF10A-Er-Src	breast:	n/a	chr12:106642719-106642730
27	POLR2A	chr12:106640778-106643389	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr12:106641501-106643421	SK-N-MC	brain:	n/a	n/a
29	POLR2A	chr12:106640974-106643979	GM19099	blood:	n/a	n/a
30	RELA	chr12:106642244-106643934	GM19099	blood:	n/a	n/a
31	POLR2A	chr12:106641418-106643261	HUVEC	blood vessel:	n/a	n/a
32	CEBPB	chr12:106642899-106643094	HepG2	liver:	n/a	n/a
33	RELA	chr12:106642243-106643879	GM10847	blood:	n/a	n/a
34	MXI1	chr12:106640491-106643212	SK-N-SH	brain:	n/a	n/a
35	MXI1	chr12:106640532-106643318	IMR90	lung:	n/a	n/a
36	FOS	chr12:106642757-106643203	HUVEC	blood vessel:	n/a	chr12:106643103-106643111

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:106634944..106646449-chr12:106667585..106679535,27	MCF-7	breast:
2	chr12:106640063..106644049-chr12:106694395..106698756,11	MCF-7	breast:
3	chr12:106640021..106643402-chr12:106749618..106753030,5	MCF-7	breast:
4	chr12:106641882..106643930-chr12:106685440..106687264,2	MCF-7	breast:
5	chr12:106639346..106644112-chr12:106694122..106698214,13	MCF-7	breast:
6	chr12:106639673..106643649-chr12:106748400..106753718,9	MCF-7	breast:
7	chr12:106640861..106643735-chr12:106674267..106678317,3	MCF-7	breast:
8	chr12:106640559..106643459-chr12:107485293..107487296,2	K562	blood:
9	chr12:106642113..106643655-chr12:106665361..106667243,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000258355	TF binding region
CKAP4	TF binding region
ENSG00000257548	Chromatin interaction
ENSG00000166046	Chromatin interaction
ENSG00000008405	Chromatin interaction
ENSG00000136026	Chromatin interaction
ENSG00000238609	Chromatin interaction
ENSG00000013503	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12424255	1.00[ASN][1000 genomes]
rs12426038	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12426351	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17216556	1.00[ASN][1000 genomes]
rs35134798	1.00[ASN][1000 genomes]
rs3782700	1.00[ASN][1000 genomes]
rs3782702	1.00[ASN][1000 genomes]
rs73384390	0.91[AFR][1000 genomes]

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	esv1799917	chr12:106637876-106649988	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv1834434	chr12:106637876-106649988	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv3403093	chr12:106639622-106643920	Flanking Active TSS Active TSS Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv3491368	chr12:106640422-106643020	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv3491369	chr12:106640422-106643020	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106642000-106644000	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr12:106642200-106643200	Flanking Active TSS	Primary B cells from peripheral blood	blood
3	chr12:106642200-106643200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr12:106642200-106643200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:106642200-106643600	Flanking Active TSS	GM12878-XiMat	blood
6	chr12:106642200-106644200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr12:106642400-106643200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:106642400-106643200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:106642400-106643200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:106642400-106643200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
11	chr12:106642400-106643200	Flanking Active TSS	Duodenum Mucosa	Duodenum
12	chr12:106642400-106643200	Enhancers	Lung	lung
13	chr12:106642400-106643200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr12:106642400-106643200	Flanking Active TSS	Stomach Smooth Muscle	stomach
15	chr12:106642400-106643200	Flanking Active TSS	HUVEC	blood vessel
16	chr12:106642400-106643200	Flanking Active TSS	NH-A	brain
17	chr12:106642400-106643400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:106642400-106643400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
19	chr12:106642400-106644200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr12:106642600-106643200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
21	chr12:106642600-106643200	Flanking Active TSS	Liver	Liver
22	chr12:106642600-106643200	Enhancers	Brain Substantia Nigra	brain
23	chr12:106642600-106643200	Flanking Active TSS	Colonic Mucosa	Colon
24	chr12:106642600-106644000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:106642600-106644400	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr12:106642800-106643200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:106642800-106643200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr12:106642800-106643200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr12:106642800-106643200	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr12:106642800-106643200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:106642800-106643200	Enhancers	Aorta	Aorta
32	chr12:106642800-106643200	Enhancers	Esophagus	oesophagus
33	chr12:106642800-106643200	Enhancers	Fetal Brain Male	brain
34	chr12:106642800-106643200	Enhancers	Fetal Brain Female	brain
35	chr12:106642800-106643200	Enhancers	Fetal Intestine Large	intestine
36	chr12:106642800-106643200	Enhancers	Fetal Intestine Small	intestine
37	chr12:106642800-106643200	Flanking Active TSS	Fetal Kidney	kidney
38	chr12:106642800-106643200	Flanking Active TSS	Fetal Muscle Trunk	muscle
39	chr12:106642800-106643200	Bivalent Enhancer	Fetal Thymus	thymus
40	chr12:106642800-106643200	Enhancers	Right Atrium	heart
41	chr12:106642800-106643200	Enhancers	Right Ventricle	heart
42	chr12:106642800-106643200	Enhancers	HSMM	muscle
43	chr12:106642800-106643200	Active TSS	HSMMtube	muscle
44	chr12:106642800-106643200	Enhancers	NHEK	skin
45	chr12:106642800-106643400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr12:106642800-106643400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr12:106642800-106643400	Enhancers	Fetal Stomach	stomach
48	chr12:106642800-106643400	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr12:106642800-106643400	Bivalent Enhancer	HepG2	liver
50	chr12:106642800-106643600	Enhancers	Primary T helper naive cells from peripheral blood	blood

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