Variant report

Variant	rs55899243
Chromosome Location	chr12:86260299-86260300
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:85968890..85970646-chr12:86260113..86261752,8	MCF-7	breast:

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1800832	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55644633	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55694421	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55736533	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55746689	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55754162	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55811116	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55811700	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55853578	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55856700	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55900789	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55926212	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55966514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56055322	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56080507	0.84[EUR][1000 genomes]
rs56145432	0.84[EUR][1000 genomes]
rs56169451	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56208754	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56298026	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56323012	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61928894	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61928895	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61928896	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61928898	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61928900	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61928903	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61928904	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61928908	0.97[EUR][1000 genomes]
rs61928913	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61928917	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61928918	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61928956	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61928957	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61928958	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61928959	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61930060	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61930061	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61930062	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61930069	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61930070	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61930071	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61930072	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61930073	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61930075	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61930079	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61930080	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61930082	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61930122	0.91[EUR][1000 genomes]
rs61930124	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61930128	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61930130	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61930131	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61930135	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61930136	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61930578	0.82[EUR][1000 genomes]
rs61930583	0.81[EUR][1000 genomes]
rs61930594	0.83[EUR][1000 genomes]
rs61930596	0.83[EUR][1000 genomes]
rs61930597	0.84[EUR][1000 genomes]
rs61930598	0.84[EUR][1000 genomes]
rs61930627	0.84[EUR][1000 genomes]
rs61930642	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61930643	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61930649	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61930651	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61930652	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61930653	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61930863	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61930876	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61930878	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61930880	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61930881	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61930882	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61930895	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7132746	0.88[EUR][1000 genomes]
rs7962310	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7973110	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052187	chr12:85954455-86278200	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv541560	chr12:85954455-86278200	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1049179	chr12:86056376-86799188	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1049443	chr12:86185887-86272493	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
5	esv1797806	chr12:86198935-86425608	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1036914	chr12:86201703-86272493	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86254800-86260800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:86259600-86260800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr12:86259600-86261400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:86259600-86261400	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr12:86259800-86260800	Enhancers	Muscle Satellite Cultured Cells	--
6	chr12:86259800-86260800	Enhancers	Adipose Nuclei	Adipose
7	chr12:86259800-86260800	Enhancers	Fetal Muscle Trunk	muscle
8	chr12:86259800-86261400	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr12:86260000-86260800	Weak transcription	Right Atrium	heart
10	chr12:86260200-86260600	Weak transcription	Fetal Intestine Small	intestine

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