Variant report

Variant	rs72954825
Chromosome Location	chr3:53389140-53389141
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53385641..53387258-chr3:53387777..53390363,2	MCF-7	breast:
2	chr3:53381505..53383202-chr3:53387994..53390796,2	K562	blood:
3	chr3:53381227..53384117-chr3:53389064..53391708,2	MCF-7	breast:
4	chr3:53368645..53370641-chr3:53389075..53391767,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162290	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11919567	1.00[AMR][1000 genomes]
rs11920772	1.00[AMR][1000 genomes]
rs11921961	1.00[AMR][1000 genomes]
rs11925433	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17030942	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17052997	1.00[AMR][1000 genomes]
rs17053116	1.00[AMR][1000 genomes]
rs58338691	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58488663	1.00[AMR][1000 genomes]
rs59254994	1.00[AMR][1000 genomes]
rs59437060	1.00[AMR][1000 genomes]
rs60350276	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60675461	1.00[AMR][1000 genomes]
rs61299945	1.00[AMR][1000 genomes]
rs6787817	1.00[AMR][1000 genomes]
rs68140464	1.00[AMR][1000 genomes]
rs72954817	1.00[AMR][1000 genomes]
rs72954820	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72954827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72954837	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72957594	1.00[AMR][1000 genomes]
rs72964389	1.00[AMR][1000 genomes]
rs72964394	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	nsv876801	chr3:53325905-53467506	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	nsv876802	chr3:53325905-53470863	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53385200-53389200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr3:53385400-53390600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:53387200-53392800	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr3:53388200-53390400	Enhancers	HUVEC	blood vessel
5	chr3:53388600-53389200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:53388600-53389400	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr3:53388600-53389400	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr3:53388600-53389600	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr3:53388600-53389800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:53388600-53389800	Enhancers	NH-A	brain
11	chr3:53388600-53390200	Enhancers	Primary hematopoietic stem cells	blood
12	chr3:53388600-53390800	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr3:53388800-53389400	Enhancers	HMEC	breast
14	chr3:53388800-53389800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:53388800-53389800	Enhancers	K562	blood
16	chr3:53388800-53390400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:53388800-53390400	Enhancers	Hela-S3	cervix
18	chr3:53389000-53389200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:53389000-53389400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:53389000-53389600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:53389000-53389600	Enhancers	NHEK	skin
22	chr3:53389000-53389600	Enhancers	Osteobl	bone
23	chr3:53389000-53389800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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