Variant report

Variant	rs56345648
Chromosome Location	chr12:123007838-123007839
allele	A/G
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	POLR2A	chr12:123007627-123008221	GM12891	blood:	n/a	n/a
2	MAX	chr12:123007828-123008192	K562	blood:	n/a	n/a
3	CEBPB	chr12:123007752-123008354	A549	lung:	n/a	chr12:123008013-123008024
4	POLR2A	chr12:123007658-123008203	K562	blood:	n/a	n/a
5	CEBPB	chr12:123007836-123008214	Hela-S3	cervix:	n/a	chr12:123008013-123008024
6	POLR2A	chr12:123007775-123008135	HepG2	liver:	n/a	n/a
7	POLR2A	chr12:123007311-123008319	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:123006664-123009749	H1-hESC	embryonic stem cell:	n/a	n/a
9	CEBPD	chr12:123007831-123008273	K562	blood:	n/a	n/a
10	POLR2A	chr12:123007693-123008181	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr12:123006600-123009349	HepG2	liver:	n/a	n/a
12	POLR2A	chr12:123007713-123008277	U87	brain:	n/a	n/a
13	CEBPB	chr12:123007815-123008274	K562	blood:	n/a	chr12:123008013-123008024
14	POLR2A	chr12:123007277-123009695	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:123007805-123008191	H1-hESC	embryonic stem cell:	n/a	n/a
16	CEBPB	chr12:123007829-123008206	HepG2	liver:	n/a	chr12:123008013-123008024
17	POLR2A	chr12:123007599-123008262	GM12892	blood:	n/a	n/a
18	POLR2A	chr12:123007534-123008195	GM12892	blood:	n/a	n/a
19	CEBPB	chr12:123007822-123008227	K562	blood:	n/a	chr12:123008013-123008024
20	POLR2A	chr12:123007699-123008121	HepG2	liver:	n/a	n/a
21	POLR2A	chr12:123007557-123008327	GM12892	blood:	n/a	n/a
22	CEBPB	chr12:123007821-123008216	IMR90	lung:	n/a	chr12:123008013-123008024
23	POLR2A	chr12:123006458-123009313	K562	blood:	n/a	n/a
24	POLR2A	chr12:123007823-123008141	GM12891	blood:	n/a	n/a
25	MXI1	chr12:123007674-123009676	IMR90	lung:	n/a	n/a
26	POLR2A	chr12:123007807-123008169	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr12:123007709-123008267	GM12891	blood:	n/a	n/a
28	POLR2A	chr12:123007719-123008144	PFSK-1	brain:	n/a	n/a
29	POLR2A	chr12:123007598-123008166	GM12891	blood:	n/a	n/a
30	POLR2A	chr12:123007757-123008119	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr12:123007817-123008212	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr12:123007325-123008356	SK-N-MC	brain:	n/a	n/a
33	CEBPB	chr12:123007834-123008208	HepG2	liver:	n/a	chr12:123008013-123008024
34	POLR2A	chr12:123007515-123008304	GM12892	blood:	n/a	n/a
35	POLR2A	chr12:123007423-123008716	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr12:123007228-123008340	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:122883163..122885704-chr12:123007231..123009242,2	K562	blood:
2	chr12:122906376..122908610-chr12:123005657..123008137,3	MCF-7	breast:
3	chr12:122963976..122966781-chr12:123007463..123009928,2	K562	blood:
4	chr12:122982366..122988748-chr12:123005500..123012938,17	MCF-7	breast:

Variant related genes	Relation type
RSRC2	TF binding region
KNTC1	TF binding region
ENSG00000033030	Chromatin interaction
ENSG00000130779	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs56882949	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58158680	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58862482	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59060380	1.00[AMR][1000 genomes]
rs60133756	0.85[AFR][1000 genomes]
rs7132364	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7135827	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7298781	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7307858	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7962592	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899570	chr12:122985057-123089209	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1041677	chr12:122991478-123114125	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	64 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	chr12:122986800-123009400	Strong transcription	Fetal Muscle Trunk	muscle
2	chr12:122987600-123008000	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr12:122987800-123008200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
4	chr12:122990000-123008200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:122998600-123008800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:123003200-123009400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
7	chr12:123003600-123008400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:123004000-123008000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
9	chr12:123004600-123008400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:123005000-123008400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr12:123005400-123009600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
12	chr12:123006000-123008600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr12:123006400-123008000	Genic enhancers	Brain Inferior Temporal Lobe	brain
14	chr12:123006400-123008200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:123006400-123008200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr12:123006400-123008200	Genic enhancers	HepG2	liver
17	chr12:123006400-123008400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:123006400-123008800	Genic enhancers	Liver	Liver
19	chr12:123006600-123008200	Genic enhancers	Fetal Intestine Small	intestine
20	chr12:123006600-123008400	Genic enhancers	Primary T cells from cord blood	blood
21	chr12:123006600-123008600	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr12:123006800-123008200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
23	chr12:123006800-123008400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr12:123006800-123008400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr12:123006800-123008800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr12:123006800-123009800	Genic enhancers	Primary B cells from peripheral blood	blood
27	chr12:123006800-123012200	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr12:123007000-123008000	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr12:123007000-123008000	Enhancers	Colon Smooth Muscle	Colon
30	chr12:123007000-123008200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:123007000-123008200	Enhancers	Fetal Heart	heart
32	chr12:123007000-123008400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:123007000-123008600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr12:123007000-123008600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
35	chr12:123007000-123009400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr12:123007200-123008400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:123007200-123008600	Enhancers	Fetal Kidney	kidney
38	chr12:123007200-123008800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr12:123007200-123008800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr12:123007200-123009600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr12:123007200-123009600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr12:123007200-123009600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:123007200-123012800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:123007400-123008000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr12:123007400-123008000	Genic enhancers	Thymus	Thymus
46	chr12:123007400-123008200	Flanking Active TSS	Brain Germinal Matrix	brain
47	chr12:123007400-123008200	Enhancers	Brain Substantia Nigra	brain
48	chr12:123007400-123008200	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
49	chr12:123007400-123008600	Genic enhancers	HSMM	muscle
50	chr12:123007400-123009600	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links