Variant report

Variant	rs10940288
Chromosome Location	chr5:52280460-52280461
allele	A/G
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	PBX3	chr5:52279932-52280528	SK-N-SH	brain:	n/a	n/a
2	STAT3	chr5:52280161-52280493	MCF10A-Er-Src	breast:	n/a	chr5:52280342-52280353 chr5:52280422-52280433
3	STAT3	chr5:52280179-52280472	MCF10A-Er-Src	breast:	n/a	chr5:52280342-52280353 chr5:52280422-52280433
4	STAT3	chr5:52280108-52280485	MCF10A-Er-Src	breast:	n/a	chr5:52280342-52280353 chr5:52280422-52280433

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

Variant related genes	Relation type
ITGA2	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11954863	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12655582	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1421940	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62357176	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62357178	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62357179	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62357180	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62357181	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357182	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357183	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62360261	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs716436	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72758633	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72758635	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][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:20 , 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	chr5:52279200-52283400	Enhancers	HMEC	breast
5	chr5:52279200-52284000	Enhancers	NHEK	skin
6	chr5:52279200-52284200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:52279400-52281600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:52279400-52281600	Enhancers	NHDF-Ad	bronchial
9	chr5:52279400-52282200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:52279400-52283200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:52279400-52283200	Enhancers	Hela-S3	cervix
12	chr5:52279400-52283400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:52279600-52280800	Enhancers	A549	lung
14	chr5:52279600-52280800	Enhancers	NHLF	lung
15	chr5:52279800-52280600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:52279800-52280600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr5:52279800-52281200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr5:52280000-52281200	Weak transcription	Osteobl	bone
19	chr5:52280200-52283200	Weak transcription	NH-A	brain
20	chr5:52280400-52280800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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