Variant report

Variant	rs10948858
Chromosome Location	chr6:54689253-54689254
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:54688351..54691007-chr6:54693141..54697889,4	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10456175	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12190982	0.82[EUR][1000 genomes]
rs12195610	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12196417	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12197945	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12198000	0.94[EUR][1000 genomes]
rs12198696	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12199020	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12203906	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12203996	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12204479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12205707	0.89[EUR][1000 genomes]
rs12209581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12210433	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12211620	0.94[EUR][1000 genomes]
rs12215996	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12216148	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12216154	0.94[EUR][1000 genomes]
rs12216371	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28819710	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3913635	0.94[EUR][1000 genomes]
rs6904875	1.00[EUR][1000 genomes]
rs6915978	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72955751	1.00[EUR][1000 genomes]
rs72955777	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72955781	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72955782	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72957543	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72957545	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72957569	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72957574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72957593	0.83[EUR][1000 genomes]
rs72967427	0.94[EUR][1000 genomes]
rs72967428	0.88[EUR][1000 genomes]
rs7745529	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7745648	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7751328	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9464136	0.94[EUR][1000 genomes]
rs9474995	0.89[EUR][1000 genomes]
rs9475003	0.94[EUR][1000 genomes]
rs9475012	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9475015	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9475016	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9475022	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9475023	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9475025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9475053	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54683400-54689600	Weak transcription	Pancreas	Pancrea
2	chr6:54689000-54689400	Enhancers	Esophagus	oesophagus
3	chr6:54689000-54689800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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