Variant report

Variant	rs12200933
Chromosome Location	chr6:81249263-81249264
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	chr6:81249220..81251616-chr6:81254290..81256470,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10943716	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10943717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10943718	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12195347	0.82[AFR][1000 genomes]
rs13212000	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1657308	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1698340	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2168104	0.91[EUR][1000 genomes]
rs2322840	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2322841	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2503719	0.97[EUR][1000 genomes]
rs2653481	0.83[EUR][1000 genomes]
rs2917599	0.98[EUR][1000 genomes]
rs2917601	0.94[EUR][1000 genomes]
rs4455626	0.96[EUR][1000 genomes]
rs4481396	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4612123	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs480295	0.82[AFR][1000 genomes]
rs484019	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs504505	0.98[EUR][1000 genomes]
rs546848	0.82[AFR][1000 genomes]
rs559528	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs565531	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs585401	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs591403	0.97[EUR][1000 genomes]
rs600262	0.97[EUR][1000 genomes]
rs607208	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62406533	0.83[AFR][1000 genomes]
rs630692	0.97[EUR][1000 genomes]
rs632422	0.88[EUR][1000 genomes]
rs643557	0.97[EUR][1000 genomes]
rs652200	0.98[EUR][1000 genomes]
rs667882	0.86[AFR][1000 genomes]
rs668698	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs676224	0.97[EUR][1000 genomes]
rs682310	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs683706	0.83[AFR][1000 genomes]
rs6933382	0.83[AFR][1000 genomes]
rs6936716	0.83[AFR][1000 genomes]
rs7738465	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9443791	0.97[EUR][1000 genomes]
rs9443797	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9449059	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9449060	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9449061	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9449063	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9449067	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9449068	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9449080	0.81[EUR][1000 genomes]
rs9449091	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531333	chr6:81042427-81836484	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1019670	chr6:81086504-81569984	ZNF genes & repeats Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv915714	chr6:81134888-81366749	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv886312	chr6:81166178-81309481	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv463908	chr6:81232993-81287675	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv604054	chr6:81232993-81287675	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3366641	chr6:81246933-81250331	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3389701	chr6:81247483-81250381	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:81233600-81249600	Weak transcription	HSMM	muscle
2	chr6:81234200-81249600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr6:81246000-81250000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:81247400-81250000	Weak transcription	Osteobl	bone
5	chr6:81247400-81250200	Weak transcription	NHDF-Ad	bronchial
6	chr6:81247600-81249800	Weak transcription	Hela-S3	cervix
7	chr6:81247600-81250400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:81247800-81249600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:81247800-81249600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:81247800-81249600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr6:81248000-81249600	Weak transcription	HMEC	breast

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