Variant report

Variant	rs4889090
Chromosome Location	chr16:80099239-80099240
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:80061244..80063092-chr16:80096922..80099593,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1115722	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11645922	0.90[EUR][1000 genomes]
rs12716881	0.84[EUR][1000 genomes]
rs12921255	0.90[EUR][1000 genomes]
rs13333795	0.89[EUR][1000 genomes]
rs1478505	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1478506	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2042362	0.83[EUR][1000 genomes]
rs2199645	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4354957	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4365299	0.90[CEU][hapmap];0.88[CHB][hapmap];0.80[JPT][hapmap];0.87[EUR][1000 genomes]
rs4402582	0.90[EUR][1000 genomes]
rs4407073	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs4500741	0.95[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes]
rs4500745	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4888067	0.90[EUR][1000 genomes]
rs4889067	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs4889068	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs4889076	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs4889084	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889086	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889092	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4889093	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6564727	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6564728	0.95[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6564729	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6564730	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7185080	0.90[EUR][1000 genomes]
rs7192544	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7192753	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7193465	0.85[EUR][1000 genomes]
rs8045670	0.98[ASN][1000 genomes]
rs8050142	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8050160	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8050173	0.87[EUR][1000 genomes]
rs8059251	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9937844	0.90[CEU][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv573285	chr16:79158182-80127326	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv573294	chr16:80005642-80131944	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv906995	chr16:80094975-80166677	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:80097800-80099600	Enhancers	Fetal Lung	lung
2	chr16:80098400-80099400	Weak transcription	Small Intestine	intestine
3	chr16:80099000-80099800	Enhancers	HMEC	breast
4	chr16:80099200-80099600	Enhancers	H1 Cell Line	embryonic stem cell
5	chr16:80099200-80099600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr16:80099200-80099800	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr16:80099200-80099800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr16:80099200-80100600	Weak transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links