Variant report

Variant	rs560201439
Chromosome Location	chr12:106642782-106642783
allele	A/G
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:10)
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	STAT3	chr12:106642719-106643018	MCF10A-Er-Src	breast:	n/a	n/a
5	SIN3A	chr12:106641582-106643087	H1-hESC	embryonic stem cell:	n/a	chr12:106641703-106641716 chr12:106641733-106641742
6	POLR2A	chr12:106641025-106644169	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:106641115-106643709	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr12:106642777-106642792	ProgFib	skin:	n/a	n/a
9	CHD1	chr12:106639633-106643296	IMR90	lung:	n/a	chr12:106641025-106641035
10	POLR2A	chr12:106641063-106643175	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr12:106641448-106643261	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr12:106640980-106642816	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:106640869-106644014	GM18951	blood:	n/a	n/a
14	RELA	chr12:106642205-106643879	GM15510	blood:	n/a	n/a
15	POLR2A	chr12:106639680-106643402	IMR90	lung:	n/a	n/a
16	MAZ	chr12:106639576-106643317	IMR90	lung:	n/a	chr12:106641917-106641927
17	POLR2A	chr12:106641586-106643325	HepG2	liver:	n/a	n/a
18	POLR2A	chr12:106642213-106643167	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr12:106640930-106644009	GM12892	blood:	n/a	n/a
20	STAT3	chr12:106642407-106643133	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr12:106640929-106644016	GM15510	blood:	n/a	n/a
22	FOS	chr12:106642653-106643078	MCF10A-Er-Src	breast:	n/a	chr12:106642719-106642730
23	POLR2A	chr12:106640778-106643389	MCF10A-Er-Src	breast:	n/a	n/a
24	MXI1	chr12:106642327-106642833	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr12:106641501-106643421	SK-N-MC	brain:	n/a	n/a
26	RUNX3	chr12:106642245-106642921	GM12878	blood:	n/a	n/a
27	FOS	chr12:106642775-106642811	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr12:106640974-106643979	GM19099	blood:	n/a	n/a
29	RELA	chr12:106642244-106643934	GM19099	blood:	n/a	n/a
30	POLR2A	chr12:106641418-106643261	HUVEC	blood vessel:	n/a	n/a
31	RELA	chr12:106642243-106643879	GM10847	blood:	n/a	n/a
32	ZNF143	chr12:106642200-106642803	GM12878	blood:	n/a	n/a
33	MXI1	chr12:106640491-106643212	SK-N-SH	brain:	n/a	n/a
34	MXI1	chr12:106640532-106643318	IMR90	lung:	n/a	n/a
35	FOS	chr12:106642757-106643203	HUVEC	blood vessel:	n/a	chr12:106643103-106643111
36	BACH1	chr12:106642177-106642831	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:10 , 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	chr12:106531582..106534564-chr12:106638638..106642825,4	MCF-7	breast:
10	chr12:106642113..106643655-chr12:106665361..106667243,2	MCF-7	breast:

No data

Variant related genes	Relation type
CKAP4	TF binding region
ENSG00000258355	TF binding region
ENSG00000238609	Chromatin interaction
ENSG00000013503	Chromatin interaction
ENSG00000008405	Chromatin interaction
ENSG00000074590	Chromatin interaction
ENSG00000257548	Chromatin interaction
ENSG00000136026	Chromatin interaction
ENSG00000166046	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 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	esv3377942	chr12:106640247-106642795	Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	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
6	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
7	esv3372615	chr12:106640922-106642870	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh 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:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106639200-106642800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr12:106639800-106643000	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr12:106640000-106642800	Active TSS	Brain Anterior Caudate	brain
4	chr12:106640000-106643000	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr12:106640000-106643000	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr12:106640200-106642800	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr12:106640200-106642800	Active TSS	Right Ventricle	heart
8	chr12:106640200-106643000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:106640400-106642800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:106640400-106642800	Active TSS	Fetal Brain Female	brain
11	chr12:106640400-106643000	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr12:106640400-106643000	Active TSS	H9 Cell Line	embryonic stem cell
13	chr12:106640600-106642800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:106640600-106642800	Active TSS	Aorta	Aorta
15	chr12:106640600-106642800	Active TSS	Brain Angular Gyrus	brain
16	chr12:106640600-106643000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:106640600-106643000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:106640800-106642800	Active TSS	Colon Smooth Muscle	Colon
19	chr12:106640800-106642800	Active TSS	Psoas Muscle	Psoas
20	chr12:106640800-106643000	Active TSS	Rectal Smooth Muscle	rectum
21	chr12:106641000-106643000	Active TSS	Adipose Nuclei	Adipose
22	chr12:106641000-106643000	Active TSS	Brain Cingulate Gyrus	brain
23	chr12:106641200-106642800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:106641200-106643000	Active TSS	Primary T cells from cord blood	blood
25	chr12:106642000-106642800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr12:106642000-106643000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:106642000-106643000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:106642000-106644000	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr12:106642200-106642800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
30	chr12:106642200-106642800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
31	chr12:106642200-106642800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr12:106642200-106642800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr12:106642200-106642800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr12:106642200-106642800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:106642200-106642800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:106642200-106642800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:106642200-106642800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:106642200-106642800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr12:106642200-106642800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
40	chr12:106642200-106642800	Flanking Active TSS	Placenta	Placenta
41	chr12:106642200-106642800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
42	chr12:106642200-106642800	Flanking Bivalent TSS/Enh	Thymus	Thymus
43	chr12:106642200-106642800	Flanking Active TSS	NHEK	skin
44	chr12:106642200-106643000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
45	chr12:106642200-106643000	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr12:106642200-106643000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr12:106642200-106643000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
48	chr12:106642200-106643000	Flanking Active TSS	Brain Germinal Matrix	brain
49	chr12:106642200-106643200	Flanking Active TSS	Primary B cells from peripheral blood	blood
50	chr12:106642200-106643200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links