Variant report

Variant	rs12298127
Chromosome Location	chr12:56280892-56280893
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:56279349..56281773-chr12:56292727..56294743,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257569	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10128982	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1052206	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.95[TSI][hapmap]
rs10747760	0.83[AMR][1000 genomes]
rs10783774	0.80[EUR][1000 genomes]
rs10783775	1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10876858	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876861	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10876862	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11171688	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1136082	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12320309	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12817350	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12824144	1.00[YRI][hapmap]
rs12827688	1.00[YRI][hapmap]
rs1463592	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1681070	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1681082	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1701698	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1701699	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1807168	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2101718	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4414258	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6581086	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6581087	0.88[AMR][1000 genomes]
rs705711	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs705715	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7068	1.00[YRI][hapmap]
rs7135133	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7297871	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs7302957	0.94[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap]
rs7308505	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs772461	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs772462	0.80[AMR][1000 genomes]
rs772468	0.84[AMR][1000 genomes]
rs772473	0.83[AMR][1000 genomes]
rs772475	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs772700	0.86[ASW][hapmap];0.94[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs772704	0.94[CEU][hapmap]
rs7979046	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9739192	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9739196	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv719	chr12:56246405-56290812	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
3	esv3347258	chr12:56267734-56298106	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56270600-56292600	Weak transcription	HSMMtube	muscle
2	chr12:56273800-56292600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:56277000-56292600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:56279800-56320000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:56280000-56294200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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