Variant report

Variant	rs6564728
Chromosome Location	chr16:80096832-80096833
allele	C/T
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	GATA3	chr16:80096736-80097221	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000260706	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10438631	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1115722	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11645922	0.88[EUR][1000 genomes]
rs12716881	0.84[EUR][1000 genomes]
rs12921255	0.88[EUR][1000 genomes]
rs13333795	0.89[EUR][1000 genomes]
rs1382387	0.95[CHB][hapmap]
rs1478505	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1478506	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2042362	0.83[EUR][1000 genomes]
rs2199645	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4354957	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4365299	0.82[CEU][hapmap];0.85[JPT][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs4402582	0.90[EUR][1000 genomes]
rs4407073	0.87[CEU][hapmap]
rs4500741	0.86[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4500745	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4888067	0.87[EUR][1000 genomes]
rs4889067	0.82[CEU][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs4889068	0.82[CEU][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs4889076	0.95[JPT][hapmap]
rs4889084	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4889086	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4889090	0.95[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4889092	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4889093	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6564727	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6564729	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6564730	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7185080	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7192544	0.95[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7192753	1.00[CEU][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7193465	0.82[EUR][1000 genomes]
rs8045670	0.82[ASN][1000 genomes]
rs8050142	0.90[ASW][hapmap];0.95[CEU][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8050160	0.95[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8050173	0.84[EUR][1000 genomes]
rs8059251	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9937844	0.82[CEU][hapmap];0.94[TSI][hapmap];0.89[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6564728	RFWD3	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:80092600-80097000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr16:80094000-80097400	Weak transcription	Small Intestine	intestine
3	chr16:80095800-80099200	Enhancers	Fetal Stomach	stomach
4	chr16:80096600-80097600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr16:80096800-80097200	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr16:80096800-80097200	Enhancers	Liver	Liver
7	chr16:80096800-80097400	Enhancers	Fetal Lung	lung
8	chr16:80096800-80097600	Enhancers	Right Atrium	heart
9	chr16:80096800-80098600	Enhancers	Fetal Intestine Large	intestine
10	chr16:80096800-80098800	Enhancers	Fetal Intestine Small	intestine

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