Variant report

Variant	rs6479302
Chromosome Location	chr9:108001966-108001967
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:107940503..107943393-chr9:108000733..108002997,2	MCF-7	breast:
2	chr9:107999147..108002971-chr9:108003945..108007816,6	MCF-7	breast:
3	chr9:107997912..108002258-chr9:108004974..108009513,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000070214	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10122513	1.00[EUR][1000 genomes]
rs12341869	0.84[ASW][hapmap];0.83[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs28688962	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs57877883	0.83[AMR][1000 genomes]
rs59290851	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6479300	1.00[AFR][1000 genomes]
rs6479301	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479303	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6479304	1.00[ASW][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7024012	0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7026389	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7031663	1.00[CEU][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs7033929	0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7039638	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7046185	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7048497	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72742562	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72744219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72744222	1.00[EUR][1000 genomes]
rs72744225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72744226	0.84[EUR][1000 genomes]
rs72744228	0.92[EUR][1000 genomes]
rs73510211	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73510218	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73510246	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73510280	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73510281	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73510289	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73510295	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73666622	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73666624	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73666625	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7847744	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7847952	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7849463	1.00[EUR][1000 genomes]
rs7853038	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7854064	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7854282	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7857088	1.00[CEU][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7860356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7869261	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7873924	0.95[YRI][hapmap]
rs7874307	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9777083	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046935	chr9:107414720-108028061	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv831678	chr9:107923522-108112813	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv893685	chr9:107940737-108083485	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1043466	chr9:107950174-108001988	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv893686	chr9:107968330-108083485	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv893687	chr9:107973277-108083485	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv893688	chr9:107974761-108083485	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv893689	chr9:107978563-108130606	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv893690	chr9:107992706-108083485	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv893691	chr9:107994629-108020284	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 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	chr9:107987800-108002400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr9:107996400-108003400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr9:107996600-108002000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr9:107996600-108002800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr9:108000000-108005200	Weak transcription	Stomach Mucosa	stomach
6	chr9:108000000-108006000	Weak transcription	Fetal Intestine Small	intestine
7	chr9:108001000-108003600	Weak transcription	HepG2	liver
8	chr9:108001200-108006000	Weak transcription	Liver	Liver
9	chr9:108001200-108006000	Weak transcription	Fetal Intestine Large	intestine
10	chr9:108001800-108003000	Weak transcription	Fetal Brain Male	brain

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