Variant report

Variant	rs9843220
Chromosome Location	chr3:120003144-120003145
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	chr3:120002820..120005702-chr3:120066388..120068289,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163428	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10934526	0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10934527	0.91[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs1118199	0.80[ASN][1000 genomes]
rs11705881	0.90[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs11706014	0.94[ASN][1000 genomes]
rs11707599	0.85[ASN][1000 genomes]
rs12638442	0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs1388754	0.81[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs1492272	0.82[CEU][hapmap]
rs1873652	0.88[ASN][1000 genomes]
rs1873653	0.84[ASN][1000 genomes]
rs2101657	0.94[ASN][1000 genomes]
rs2131176	0.94[ASN][1000 genomes]
rs2319669	0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2319670	0.81[EUR][1000 genomes]
rs2319671	0.94[ASN][1000 genomes]
rs2319672	0.90[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs4146299	0.85[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs4146300	0.85[CEU][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs4378995	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771116	0.81[EUR][1000 genomes]
rs6771865	0.85[JPT][hapmap]
rs6774960	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795868	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72954789	0.94[ASN][1000 genomes]
rs9816153	0.85[JPT][hapmap]
rs9824334	0.88[ASN][1000 genomes]
rs9848714	0.94[ASN][1000 genomes]
rs9849695	0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs9856288	0.88[ASN][1000 genomes]
rs9856618	0.82[ASN][1000 genomes]
rs9875613	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv829698	chr3:119960869-120129126	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	esv2763294	chr3:119994092-120003434	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120000600-120003400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr3:120002000-120003200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
3	chr3:120002400-120003200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
4	chr3:120002600-120003400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr3:120002600-120003600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:120002800-120003200	Enhancers	H9 Cell Line	embryonic stem cell
7	chr3:120002800-120003400	Enhancers	Brain Germinal Matrix	brain
8	chr3:120003000-120003200	Active TSS	Fetal Brain Female	brain
9	chr3:120003000-120003400	Enhancers	Colon Smooth Muscle	Colon
10	chr3:120003000-120004600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell

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