Variant report

Variant	rs10880331
Chromosome Location	chr12:43016780-43016781
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	chr12:43014304..43016802-chr12:43019715..43022401,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257687	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10736003	1.00[CEU][hapmap]
rs10785355	0.84[AFR][1000 genomes]
rs10785356	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10785358	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11181583	0.90[AFR][1000 genomes]
rs12422484	0.90[EUR][1000 genomes]
rs12423156	0.85[EUR][1000 genomes]
rs12423337	0.85[EUR][1000 genomes]
rs12423346	0.85[EUR][1000 genomes]
rs12423349	0.85[EUR][1000 genomes]
rs12423470	0.89[EUR][1000 genomes]
rs12423824	0.90[EUR][1000 genomes]
rs12424138	0.97[EUR][1000 genomes]
rs12424455	0.97[EUR][1000 genomes]
rs12424504	0.97[EUR][1000 genomes]
rs12424511	0.97[EUR][1000 genomes]
rs12424763	0.97[EUR][1000 genomes]
rs12424886	0.97[EUR][1000 genomes]
rs12425177	0.97[EUR][1000 genomes]
rs12425193	0.97[EUR][1000 genomes]
rs12425470	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12425775	0.97[EUR][1000 genomes]
rs12426290	0.97[EUR][1000 genomes]
rs12426303	0.97[EUR][1000 genomes]
rs12426479	0.90[EUR][1000 genomes]
rs12426718	0.89[EUR][1000 genomes]
rs12426988	0.97[EUR][1000 genomes]
rs12827135	0.85[EUR][1000 genomes]
rs17091490	0.85[EUR][1000 genomes]
rs17091505	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1882663	0.81[AFR][1000 genomes]
rs1922756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2178751	0.85[EUR][1000 genomes]
rs2406858	0.97[EUR][1000 genomes]
rs2406861	0.85[EUR][1000 genomes]
rs2406862	0.85[EUR][1000 genomes]
rs2897539	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4238085	0.85[EUR][1000 genomes]
rs4321015	0.85[EUR][1000 genomes]
rs4590936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4768425	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs57263961	0.96[EUR][1000 genomes]
rs57908879	0.97[EUR][1000 genomes]
rs60211398	0.97[EUR][1000 genomes]
rs60670517	0.83[EUR][1000 genomes]
rs60776045	0.96[EUR][1000 genomes]
rs7131974	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7133039	0.97[EUR][1000 genomes]
rs7133172	0.97[EUR][1000 genomes]
rs7133774	0.97[EUR][1000 genomes]
rs7296915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301558	0.82[EUR][1000 genomes]
rs7303511	0.90[EUR][1000 genomes]
rs7304849	0.97[EUR][1000 genomes]
rs7306530	0.90[EUR][1000 genomes]
rs7306683	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7307159	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7314565	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7952819	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7959843	0.85[EUR][1000 genomes]
rs7964774	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7976696	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7980015	0.84[AFR][1000 genomes]
rs9988993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
3	nsv832388	chr12:42878328-43087069	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv832389	chr12:43003361-43173896	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv558702	chr12:43015354-43027352	Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv558703	chr12:43015532-43025256	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv558704	chr12:43015532-43027453	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:43016200-43017000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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