Variant report

Variant	rs12298136
Chromosome Location	chr12:56516770-56516771
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56516720-56517016	HepG2	liver:	n/a	n/a
2	RCOR1	chr12:56516606-56516805	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:56514537-56517059	SK-N-MC	brain:	n/a	n/a
4	ARID3A	chr12:56516473-56516801	HepG2	liver:	n/a	n/a
5	FOXA2	chr12:56516461-56516779	HepG2	liver:	n/a	n/a
6	FOXA1	chr12:56516501-56516856	HepG2	liver:	n/a	n/a
7	FOXA1	chr12:56516348-56516818	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:56507991..56525761-chr12:56579808..56586137,68	MCF-7	breast:
2	chr12:56433873..56442113-chr12:56515349..56524351,14	K562	blood:
3	chr12:56508092..56528020-chr12:56536122..56568603,201	MCF-7	breast:
4	chr12:56513950..56516909-chr12:56546268..56547883,2	MCF-7	breast:
5	chr12:56317848..56319643-chr12:56515602..56517864,2	K562	blood:
6	chr12:56433908..56446518-chr12:56506026..56517165,55	MCF-7	breast:
7	chr12:56514975..56517772-chr12:56694804..56696732,2	MCF-7	breast:
8	chr12:56516674..56520243-chr12:56693708..56696714,5	K562	blood:
9	chr12:56516279..56526040-chr12:56550254..56554953,37	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000258345	TF binding region
ENSG00000196465	Chromatin interaction
ENSG00000257303	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000062485	Chromatin interaction
ENSG00000257449	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10129008	0.90[AFR][1000 genomes]
rs11171746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11171754	1.00[AFR][1000 genomes]
rs11171755	1.00[AFR][1000 genomes]
rs11504023	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12296387	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12309480	0.85[AFR][1000 genomes]
rs12309692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17118317	0.90[ASN][1000 genomes]
rs28546848	0.93[AFR][1000 genomes]
rs28676339	1.00[AFR][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	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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56513000-56521000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:56513200-56520000	Weak transcription	Right Atrium	heart
3	chr12:56513400-56520200	Enhancers	HepG2	liver
4	chr12:56513600-56518800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr12:56513600-56518800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr12:56513600-56520200	Weak transcription	Fetal Brain Male	brain
7	chr12:56513800-56516800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:56513800-56516800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:56513800-56516800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
10	chr12:56513800-56517800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:56513800-56518600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr12:56513800-56519000	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr12:56513800-56519800	Weak transcription	Stomach Mucosa	stomach
14	chr12:56514000-56516800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:56514000-56516800	Strong transcription	Primary B cells from cord blood	blood
16	chr12:56514000-56516800	Strong transcription	Primary T cells from cord blood	blood
17	chr12:56514000-56516800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr12:56514000-56517000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:56514000-56517000	Strong transcription	Brain Germinal Matrix	brain
20	chr12:56514000-56517000	Strong transcription	Fetal Intestine Small	intestine
21	chr12:56514000-56517200	Strong transcription	Primary B cells from peripheral blood	blood
22	chr12:56514000-56517400	Genic enhancers	Fetal Muscle Leg	muscle
23	chr12:56514000-56517600	Strong transcription	Fetal Stomach	stomach
24	chr12:56514000-56518000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:56514000-56518200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:56514000-56518200	Strong transcription	Fetal Thymus	thymus
27	chr12:56514000-56518400	Strong transcription	Brain Anterior Caudate	brain
28	chr12:56514000-56519200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr12:56514000-56519200	Weak transcription	GM12878-XiMat	blood
30	chr12:56514000-56519800	Weak transcription	Fetal Kidney	kidney
31	chr12:56514000-56519800	Weak transcription	Fetal Lung	lung
32	chr12:56514000-56520200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr12:56514000-56520200	Weak transcription	Small Intestine	intestine
34	chr12:56514200-56516800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:56514200-56517000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:56514200-56517400	Weak transcription	K562	blood
37	chr12:56514200-56518200	Strong transcription	Brain Substantia Nigra	brain
38	chr12:56514400-56516800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr12:56514400-56516800	Strong transcription	Primary hematopoietic stem cells	blood
40	chr12:56514400-56516800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:56514400-56516800	Strong transcription	Duodenum Mucosa	Duodenum
42	chr12:56514400-56516800	Strong transcription	Fetal Brain Female	brain
43	chr12:56514400-56516800	Strong transcription	NHLF	lung
44	chr12:56514400-56517000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:56514400-56517000	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr12:56514400-56517200	Strong transcription	Dnd41	blood
47	chr12:56514400-56518800	Weak transcription	HUVEC	blood vessel
48	chr12:56514600-56519800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:56514600-56519800	Weak transcription	Hela-S3	cervix
50	chr12:56514800-56519800	Weak transcription	HMEC	breast

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