Variant report

Variant	rs12298573
Chromosome Location	chr12:56547450-56547451
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr12:56545558-56547488	IMR90	lung:	n/a	chr12:56546071-56546081 chr12:56546378-56546388
2	POLR2A	chr12:56547075-56547656	HepG2	liver:	n/a	n/a
3	HCFC1	chr12:56545106-56547524	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr12:56544990-56547644	SK-N-MC	brain:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56543805..56547677-chr12:56615744..56618519,4	MCF-7	breast:
2	chr12:56434536..56437733-chr12:56543304..56547761,4	K562	blood:
3	chr12:56543953..56550163-chr12:56578779..56585351,11	MCF-7	breast:
4	chr12:56546962..56549504-chr12:56614764..56616913,2	MCF-7	breast:
5	chr12:56509009..56513573-chr12:56543891..56549811,15	MCF-7	breast:
6	chr12:56508092..56528020-chr12:56536122..56568603,201	MCF-7	breast:
7	chr12:56544479..56547707-chr17:57917594..57920686,3	MCF-7	breast:
8	chr12:56518356..56534331-chr12:56534720..56548698,49	MCF-7	breast:
9	chr12:56435355..56437386-chr12:56546202..56547855,2	MCF-7	breast:
10	chr12:56497691..56500664-chr12:56545558..56547668,3	MCF-7	breast:
11	chr12:56471798..56475584-chr12:56544179..56549010,6	MCF-7	breast:
12	chr12:56367458..56369126-chr12:56546076..56548223,2	MCF-7	breast:

No data

Variant related genes	Relation type
MYL6B	TF binding region
MYL6	TF binding region
ENSG00000139579	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000258317	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000111540	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs11552470	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56545200-56547600	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr12:56546400-56547600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr12:56546400-56548800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
4	chr12:56546600-56547600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:56546600-56547600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
6	chr12:56546600-56547600	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr12:56546600-56547600	Enhancers	Spleen	Spleen
8	chr12:56546600-56547600	Flanking Active TSS	GM12878-XiMat	blood
9	chr12:56546600-56547800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:56546600-56547800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:56546600-56547800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:56546600-56547800	Flanking Active TSS	Brain Germinal Matrix	brain
13	chr12:56546600-56547800	Flanking Active TSS	Fetal Muscle Trunk	muscle
14	chr12:56546600-56547800	Flanking Active TSS	Dnd41	blood
15	chr12:56546600-56548000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:56546600-56548200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr12:56546600-56548600	Flanking Active TSS	HSMM	muscle
18	chr12:56546800-56547600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr12:56546800-56547600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:56546800-56547600	Enhancers	Primary B cells from cord blood	blood
21	chr12:56546800-56547600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr12:56546800-56547600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:56546800-56547600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:56546800-56547600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:56546800-56547600	Enhancers	Placenta	Placenta
26	chr12:56546800-56547600	Enhancers	Lung	lung
27	chr12:56546800-56547600	Flanking Active TSS	Hela-S3	cervix
28	chr12:56546800-56547800	Flanking Active TSS	HSMMtube	muscle
29	chr12:56546800-56548000	Flanking Active TSS	Fetal Brain Female	brain
30	chr12:56546800-56551000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr12:56546800-56551000	Weak transcription	Ovary	ovary
32	chr12:56546800-56551200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr12:56547000-56547600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:56547000-56547600	Enhancers	Colonic Mucosa	Colon
35	chr12:56547000-56547600	Enhancers	Fetal Thymus	thymus
36	chr12:56547000-56547800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr12:56547000-56547800	Enhancers	Psoas Muscle	Psoas
38	chr12:56547000-56547800	Flanking Active TSS	HepG2	liver
39	chr12:56547000-56548000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:56547000-56548000	Enhancers	Primary hematopoietic stem cells	blood
41	chr12:56547000-56548200	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr12:56547000-56548400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:56547000-56549000	Weak transcription	Primary T cells from cord blood	blood
44	chr12:56547000-56549200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr12:56547000-56550600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr12:56547000-56550600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr12:56547000-56550800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr12:56547000-56551000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr12:56547000-56551000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr12:56547000-56551000	Weak transcription	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links