Variant report

Variant	rs7299453
Chromosome Location	chr12:51741679-51741680
allele	C/T
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	chr12:51741477-51741758	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:51661897..51665217-chr12:51739188..51742261,4	MCF-7	breast:
2	chr12:51740737..51742695-chr12:51746818..51748800,2	MCF-7	breast:
3	chr12:51732471..51736842-chr12:51740584..51742945,3	MCF-7	breast:

Variant related genes	Relation type
CELA1	TF binding region
ENSG00000170545	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10516	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876162	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11169805	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11616158	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12310910	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12582273	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12829179	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12831721	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17860300	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17860301	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17860343	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3858624	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3858627	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7133606	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7138439	0.86[EUR][1000 genomes]
rs7299306	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7306746	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7959814	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7964134	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9651999	0.87[AMR][1000 genomes];0.99[EUR][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	nsv482304	chr12:51653496-51814917	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv832408	chr12:51696605-51871339	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51731800-51750600	Weak transcription	Spleen	Spleen
2	chr12:51735400-51743000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:51735400-51743000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr12:51735400-51745400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr12:51735400-51745400	Weak transcription	Brain Substantia Nigra	brain
6	chr12:51735400-51745800	Weak transcription	Fetal Intestine Small	intestine
7	chr12:51735400-51746800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:51735400-51747400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr12:51735400-51747400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:51735400-51747400	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr12:51735400-51747600	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr12:51735400-51747800	Weak transcription	NHLF	lung
13	chr12:51735400-51750200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr12:51735400-51750600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:51735400-51750600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr12:51735400-51756000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:51735600-51746800	Weak transcription	Primary T cells from cord blood	blood
18	chr12:51735600-51750600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:51735600-51761400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr12:51735800-51747400	Weak transcription	Dnd41	blood
21	chr12:51736400-51765400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:51736600-51742000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:51739400-51748400	Weak transcription	Gastric	stomach
24	chr12:51739400-51754200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr12:51739600-51744800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:51739600-51750600	Weak transcription	GM12878-XiMat	blood
27	chr12:51740000-51741800	Weak transcription	K562	blood
28	chr12:51740000-51742000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr12:51740000-51742400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:51740000-51747400	Weak transcription	NHEK	skin
31	chr12:51740200-51745800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:51740200-51746800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:51740400-51741800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr12:51740400-51747400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:51740400-51747400	Weak transcription	Thymus	Thymus
36	chr12:51740400-51747800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr12:51740600-51747600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr12:51740600-51751000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:51740800-51745200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr12:51740800-51753200	Weak transcription	NHDF-Ad	bronchial
41	chr12:51741000-51742400	Weak transcription	Osteobl	bone
42	chr12:51741000-51742800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:51741000-51744200	Enhancers	Placenta	Placenta
44	chr12:51741000-51745400	Weak transcription	Pancreas	Pancrea
45	chr12:51741000-51745600	Weak transcription	Fetal Thymus	thymus
46	chr12:51741000-51747800	Weak transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links