Variant report

Variant	rs2470820
Chromosome Location	chr3:98712810-98712811
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:98536035..98537025-chr3:98712684..98713619,5	K562	blood:
2	chr3:98536449..98537173-chr3:98712702..98713434,3	MCF-7	breast:
3	chr3:98543071..98543590-chr3:98712733..98713238,2	MCF-7	breast:
4	chr3:98543087..98543918-chr3:98712722..98713277,2	MCF-7	breast:
5	chr3:98536046..98537400-chr3:98712632..98713675,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000057019	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1082398	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1082399	1.00[EUR][1000 genomes]
rs1082400	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1082402	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1082404	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1082406	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1351496	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1383908	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1440157	0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs1481633	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1531736	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1600788	0.82[AFR][1000 genomes]
rs1818053	0.86[YRI][hapmap]
rs1972432	0.84[AFR][1000 genomes]
rs2128053	0.84[AFR][1000 genomes]
rs2133575	0.82[AFR][1000 genomes]
rs2173598	0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs2439234	0.86[YRI][hapmap]
rs2439235	0.86[YRI][hapmap]
rs2448985	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2454681	0.84[AFR][1000 genomes]
rs2454683	0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs2470828	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2470850	0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2470856	0.84[AFR][1000 genomes]
rs2470858	0.82[AFR][1000 genomes]
rs2470868	0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs2470883	0.84[AFR][1000 genomes]
rs2470884	0.82[AFR][1000 genomes]
rs278384	0.86[YRI][hapmap]
rs278385	0.86[YRI][hapmap]
rs2929491	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4273318	0.84[AFR][1000 genomes]
rs4857107	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs5013928	0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs6795351	0.85[AFR][1000 genomes]
rs73858658	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7630797	0.81[AFR][1000 genomes]
rs774536	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs774543	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs774546	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs774548	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs828606	0.85[YRI][hapmap]
rs828607	0.86[YRI][hapmap]
rs974982	0.97[AFR][1000 genomes]
rs9883226	0.86[YRI][hapmap]
rs996199	0.86[YRI][hapmap];0.82[AFR][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	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98705000-98713000	Weak transcription	HSMM	muscle
2	chr3:98705600-98716400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:98711000-98721200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:98712400-98713200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:98712400-98713200	Enhancers	NHDF-Ad	bronchial
6	chr3:98712400-98713600	Enhancers	A549	lung
7	chr3:98712400-98713800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:98712800-98713200	Enhancers	Fetal Heart	heart
9	chr3:98712800-98713200	Enhancers	HMEC	breast
10	chr3:98712800-98713200	Enhancers	NHLF	lung
11	chr3:98712800-98713200	Enhancers	Osteobl	bone
12	chr3:98712800-98723000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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