Variant report

Variant	rs16885911
Chromosome Location	chr6:54596917-54596918
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:54594502..54597427-chr6:54632424..54633945,2	MCF-7	breast:
2	chr6:54596752..54599206-chr6:54723703..54726514,2	MCF-7	breast:
3	chr6:54585837..54588493-chr6:54594744..54597239,2	MCF-7	breast:
4	chr6:54589684..54593022-chr6:54593846..54596999,3	MCF-7	breast:
5	chr6:54596908..54599664-chr6:54710614..54713357,2	MCF-7	breast:
6	chr6:54594616..54597518-chr6:54631395..54633965,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1039496	0.89[ASN][1000 genomes]
rs10948840	0.92[ASN][1000 genomes]
rs10948844	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10948846	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11967781	0.90[CHB][hapmap]
rs12525001	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs12527042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12527077	0.85[CHB][hapmap]
rs12527080	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12527124	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12528270	0.94[ASN][1000 genomes]
rs12528881	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12661998	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12662465	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1648201	0.81[ASN][1000 genomes]
rs16869519	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16885735	0.85[ASN][1000 genomes]
rs16885866	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs16885948	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1948954	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1976539	0.86[ASN][1000 genomes]
rs1983140	0.82[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs2048112	0.96[ASN][1000 genomes]
rs2048113	0.82[ASN][1000 genomes]
rs2894821	0.81[ASN][1000 genomes]
rs34752465	0.92[ASN][1000 genomes]
rs35953958	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4712068	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4712070	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs4715470	0.94[ASN][1000 genomes]
rs4715478	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4994100	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58302712	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60501416	0.92[ASN][1000 genomes]
rs67799698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67875074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6915244	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73442093	0.82[ASN][1000 genomes]
rs73444113	0.96[ASN][1000 genomes]
rs73444116	0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs73444125	0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs73446026	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73446030	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73446036	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73446043	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7751908	0.86[CHB][hapmap];0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv885901	chr6:54588069-54635417	Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv885902	chr6:54588069-54656673	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	4 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	chr6:54595600-54599800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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