Variant report

Variant	rs7297628
Chromosome Location	chr12:64404555-64404556
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:64402701..64405332-chr12:64614473..64617172,2	MCF-7	breast:
2	chr12:64236732..64239854-chr12:64401083..64405979,5	MCF-7	breast:
3	chr12:64397033..64398653-chr12:64402137..64404710,2	K562	blood:
4	chr12:64257643..64259888-chr12:64403526..64405520,2	MCF-7	breast:
5	chr12:64236584..64241512-chr12:64401758..64407787,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174206	Chromatin interaction
ENSG00000243024	Chromatin interaction
ENSG00000196935	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10784376	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10784377	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10878099	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11175237	0.93[EUR][1000 genomes]
rs11836824	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12367875	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17710730	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2335389	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35136111	0.93[EUR][1000 genomes]
rs35266586	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3930087	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6421210	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6581518	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6581520	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6581521	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6581522	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6581523	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6581524	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6581526	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6581527	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6581528	0.81[EUR][1000 genomes]
rs7295635	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7299597	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7308431	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7311377	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7312152	0.92[EUR][1000 genomes]
rs7312345	0.93[EUR][1000 genomes]
rs7316077	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7958660	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7967578	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970430	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7971280	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7974633	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7978183	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7978207	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832442	chr12:64228071-64442771	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv747	chr12:64391572-64423998	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
3	nsv437756	chr12:64392500-64411870	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
4	esv3497141	chr12:64399267-64405968	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
5	esv3497152	chr12:64399267-64405968	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
6	nsv498794	chr12:64399408-64405869	Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
7	esv15842	chr12:64399479-64405306	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
8	nsv442274	chr12:64401238-64405435	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64380200-64433000	Weak transcription	Fetal Intestine Large	intestine
2	chr12:64382800-64432800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:64383800-64425400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:64385000-64408800	Weak transcription	Hela-S3	cervix
5	chr12:64385000-64425600	Weak transcription	Left Ventricle	heart
6	chr12:64388800-64429800	Weak transcription	Pancreas	Pancrea
7	chr12:64389400-64419200	Weak transcription	Fetal Kidney	kidney
8	chr12:64389400-64419200	Weak transcription	Fetal Lung	lung
9	chr12:64389600-64417400	Weak transcription	Fetal Muscle Leg	muscle
10	chr12:64395400-64412400	Weak transcription	HMEC	breast
11	chr12:64396000-64415600	Weak transcription	Fetal Brain Female	brain
12	chr12:64396400-64414000	Weak transcription	Psoas Muscle	Psoas
13	chr12:64397200-64411200	Weak transcription	Fetal Intestine Small	intestine
14	chr12:64398000-64425200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:64398200-64404600	Enhancers	Osteobl	bone
16	chr12:64398200-64405000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr12:64399600-64404600	Enhancers	NHDF-Ad	bronchial
18	chr12:64399600-64404800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:64400000-64405000	Enhancers	NHLF	lung
20	chr12:64400400-64418400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:64400800-64407000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:64401000-64404800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr12:64401400-64404600	Enhancers	NH-A	brain
24	chr12:64401400-64416000	Weak transcription	Ovary	ovary
25	chr12:64402000-64413200	Weak transcription	NHEK	skin
26	chr12:64402000-64413400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:64402000-64415800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:64402200-64404800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:64402200-64407000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr12:64402200-64419200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:64402600-64405000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr12:64402600-64405200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:64403200-64404600	Enhancers	HepG2	liver
34	chr12:64403400-64404600	Enhancers	Fetal Heart	heart
35	chr12:64403600-64404600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr12:64403600-64404600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:64403600-64404600	Enhancers	Rectal Smooth Muscle	rectum
38	chr12:64403600-64404600	Flanking Active TSS	A549	lung
39	chr12:64403600-64405000	Enhancers	Brain Substantia Nigra	brain
40	chr12:64403800-64404600	Enhancers	Colon Smooth Muscle	Colon
41	chr12:64404000-64404600	Enhancers	Brain Hippocampus Middle	brain
42	chr12:64404200-64405800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:64404400-64404600	Enhancers	H1 Cell Line	embryonic stem cell
44	chr12:64404400-64410400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:64404400-64411000	Weak transcription	HSMM	muscle
46	chr12:64404400-64415200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr12:64404400-64417400	Weak transcription	HSMMtube	muscle

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