Variant report

Variant	rs9828077
Chromosome Location	chr3:51855143-51855144
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:51851120..51852647-chr3:51853299..51856241,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224792	Chromatin interaction
ENSG00000229972	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12631654	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12639503	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs1505404	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2102297	0.82[AFR][1000 genomes]
rs28481670	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56204016	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56285190	0.82[AMR][1000 genomes]
rs56998832	0.82[AMR][1000 genomes]
rs6446041	0.81[AFR][1000 genomes]
rs6762083	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6768073	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6798175	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6805324	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6805941	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6809548	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7639080	0.88[AFR][1000 genomes]
rs9826967	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9836804	1.00[AMR][1000 genomes]
rs9840833	0.88[AFR][1000 genomes]
rs9857964	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9866552	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9869265	0.92[AFR][1000 genomes];1.00[AMR][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	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer 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	53 gene(s)	inside rSNPs	diseases
2	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv3416846	chr3:51781117-51888179	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
5	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51852800-51855400	Weak transcription	Right Atrium	heart
2	chr3:51854600-51855200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links