Variant report

Variant	rs10880810
Chromosome Location	chr12:45924964-45924965
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:45923564..45926208-chr12:46122696..46124400,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000189079	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10785580	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs10785581	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10880808	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10880809	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10880813	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10880815	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10880816	0.83[CEU][hapmap]
rs11183092	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11183093	0.84[EUR][1000 genomes]
rs11183094	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11183097	0.87[EUR][1000 genomes]
rs11183098	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11183099	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11183101	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11183103	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes]
rs11514430	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11514431	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1806689	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs2408249	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2897908	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3958762	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs4450222	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4601849	0.84[AFR][1000 genomes]
rs4606536	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4768629	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4768631	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4768633	0.81[EUR][1000 genomes]
rs4768635	0.82[ASN][1000 genomes]
rs4768636	0.92[CEU][hapmap]
rs56295584	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61923980	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7132173	0.88[CEU][hapmap]
rs7296623	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7297465	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7303050	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7960483	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7970315	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7971648	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832395	chr12:45841765-46039297	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv508672	chr12:45884730-45931091	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv691	chr12:45896295-45946455	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv558761	chr12:45901586-45924964	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv1842210	chr12:45903118-45940761	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv3443760	chr12:45913734-45935783	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45913200-45927000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:45924600-45927600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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