Variant report

Variant	rs411254
Chromosome Location	chr21:46032094-46032095
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	chr21:46010036..46012728-chr21:46031362..46034012,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188155	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1211061	0.87[CHB][hapmap]
rs1211088	0.86[JPT][hapmap];0.82[MEX][hapmap]
rs1211089	0.84[JPT][hapmap]
rs1211103	1.00[CEU][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs1211121	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs1211123	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs12627414	0.95[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs170849	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2226687	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs233262	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs233263	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233264	0.87[CEU][hapmap];0.94[CHB][hapmap];0.95[GIH][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233265	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs233267	0.85[EUR][1000 genomes]
rs233268	0.87[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs233269	0.89[EUR][1000 genomes]
rs233270	0.87[CEU][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs233271	0.89[EUR][1000 genomes]
rs233272	0.87[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2838598	0.91[CHD][hapmap];0.82[MEX][hapmap]
rs367771	0.87[CEU][hapmap];0.94[CHB][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs369111	0.85[CHB][hapmap]
rs370092	0.90[CHD][hapmap];0.86[JPT][hapmap]
rs371248	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs377234	1.00[CEU][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs377263	1.00[CEU][hapmap]
rs379858	0.87[CHB][hapmap]
rs382935	1.00[CEU][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs384645	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs392451	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs392686	1.00[CEU][hapmap];0.95[CHD][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs398680	1.00[CEU][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs400368	0.87[CHB][hapmap]
rs400406	0.84[JPT][hapmap]
rs403981	1.00[CEU][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs404341	1.00[CEU][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs408183	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs408958	1.00[CEU][hapmap]
rs409893	0.85[JPT][hapmap]
rs415753	1.00[CEU][hapmap];0.95[CHD][hapmap];0.81[EUR][1000 genomes]
rs416056	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs417538	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs418260	0.86[JPT][hapmap];1.00[MEX][hapmap]
rs423954	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs425823	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs430609	0.87[CHB][hapmap]
rs434716	0.87[CHB][hapmap]
rs442110	0.82[EUR][1000 genomes]
rs442226	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs442600	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs445214	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs446817	1.00[CEU][hapmap]
rs451948	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs452002	1.00[CEU][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs455413	0.87[CHB][hapmap]
rs455562	0.87[CHB][hapmap]
rs455714	0.87[CHB][hapmap]
rs455777	0.87[CHB][hapmap]
rs455906	1.00[JPT][hapmap]
rs456019	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs456444	0.87[CHB][hapmap]
rs457322	0.87[CHB][hapmap]
rs459845	0.87[CHB][hapmap]
rs459915	0.87[CHB][hapmap]
rs460064	0.87[CHB][hapmap]
rs460085	0.87[CHB][hapmap]
rs460122	0.87[CHB][hapmap]
rs462254	0.87[CHB][hapmap]
rs463239	0.87[CHB][hapmap]
rs463267	0.87[CHB][hapmap]
rs463668	0.87[CHB][hapmap]
rs464281	0.87[CHB][hapmap]
rs464504	0.87[CHB][hapmap]
rs464684	0.87[CHB][hapmap]
rs465930	0.87[CHB][hapmap]
rs466094	0.87[CHB][hapmap]
rs487102	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58029281	0.81[ASN][1000 genomes]
rs659638	1.00[CEU][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs8132500	0.88[CHB][hapmap];0.95[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065798	chr21:45941000-46097463	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv869108	chr21:45941000-46097463	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv544476	chr21:45941000-46097463	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv913950	chr21:45985068-46097463	Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46018400-46048400	Weak transcription	Right Atrium	heart
2	chr21:46030800-46032200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr21:46031600-46032200	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
4	chr21:46031800-46032400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
5	chr21:46031800-46032600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr21:46031800-46032800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell

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