Variant report

Variant	rs62357199
Chromosome Location	chr5:52280107-52280108
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52278874..52281430-chr5:52281937..52284347,4	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs16876270	0.86[EUR][1000 genomes]
rs3212394	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41305896	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56719416	0.90[EUR][1000 genomes]
rs62357159	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62357175	0.86[EUR][1000 genomes]
rs62357177	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62357195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62357197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62357200	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62357202	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62357203	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62357227	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62357230	0.95[EUR][1000 genomes]
rs6450105	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52273600-52283800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:52279000-52283400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr5:52279000-52283400	Enhancers	HUVEC	blood vessel
4	chr5:52279200-52280200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr5:52279200-52280400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:52279200-52283400	Enhancers	HMEC	breast
7	chr5:52279200-52284000	Enhancers	NHEK	skin
8	chr5:52279200-52284200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:52279400-52281600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:52279400-52281600	Enhancers	NHDF-Ad	bronchial
11	chr5:52279400-52282200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:52279400-52283200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:52279400-52283200	Enhancers	Hela-S3	cervix
14	chr5:52279400-52283400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr5:52279600-52280800	Enhancers	A549	lung
16	chr5:52279600-52280800	Enhancers	NHLF	lung
17	chr5:52279800-52280200	Enhancers	NH-A	brain
18	chr5:52279800-52280600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:52279800-52280600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:52279800-52281200	Enhancers	Muscle Satellite Cultured Cells	--
21	chr5:52280000-52281200	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links