Variant report

Variant	rs9811707
Chromosome Location	chr3:52190657-52190658
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52187270..52191492-chr3:52311211..52313437,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164091	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs123681	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12386365	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13314125	0.94[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13319566	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs164638	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs164639	0.85[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.88[TSI][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17051957	0.92[ASW][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17051977	0.84[ASW][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171294	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs183029	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304505	0.84[ASW][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28452586	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28659792	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352146	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs352147	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352148	0.85[CHD][hapmap];0.89[JPT][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352149	0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352150	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352151	0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352153	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55664415	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55834589	0.88[EUR][1000 genomes]
rs56281986	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56322622	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57335685	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57466127	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59890038	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781635	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72964042	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72964044	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7638246	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808787	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs876782	0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs893056	0.92[ASW][hapmap];0.94[GIH][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9809254	0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs9809977	1.00[ASW][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.92[LWK][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815010	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816434	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9817653	1.00[ASW][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.92[LWK][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830293	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841469	0.89[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843299	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843852	0.89[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846049	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9847073	0.84[ASW][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847092	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857878	0.94[GIH][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]
rs9860982	0.81[ASW][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9865330	0.87[GIH][hapmap];0.83[TSI][hapmap]
rs9868101	0.89[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882775	0.94[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
5	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
8	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52189200-52191400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:52189400-52191000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:52189400-52191000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:52189400-52191200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:52189400-52191600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:52189400-52191600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:52189400-52191600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:52189400-52196400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:52189400-52196400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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