Variant report

Variant	rs6539686
Chromosome Location	chr12:83144385-83144386
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	chr12:83077789..83082139-chr12:83143986..83148057,5	MCF-7	breast:
2	chr12:83138681..83143794-chr12:83143962..83149750,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179104	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10506883	1.00[AMR][1000 genomes]
rs10732678	1.00[AMR][1000 genomes]
rs10746256	1.00[AMR][1000 genomes]
rs10862499	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17010020	1.00[AMR][1000 genomes]
rs17010029	1.00[AMR][1000 genomes]
rs17041817	1.00[AMR][1000 genomes]
rs2470367	1.00[AMR][1000 genomes]
rs2470368	1.00[AMR][1000 genomes]
rs2470887	1.00[AMR][1000 genomes]
rs2470888	1.00[AMR][1000 genomes]
rs4242868	1.00[AMR][1000 genomes]
rs4882525	1.00[AMR][1000 genomes]
rs56722406	1.00[AMR][1000 genomes]
rs56834199	1.00[AMR][1000 genomes]
rs57366330	1.00[AMR][1000 genomes]
rs57850546	1.00[AMR][1000 genomes]
rs61361946	1.00[AMR][1000 genomes]
rs7297682	1.00[AMR][1000 genomes]
rs7307597	1.00[AMR][1000 genomes]
rs73356400	1.00[AMR][1000 genomes]
rs73358226	1.00[AMR][1000 genomes]
rs73358227	1.00[AMR][1000 genomes]
rs73358228	1.00[AMR][1000 genomes]
rs73358233	1.00[AMR][1000 genomes]
rs73358237	1.00[AMR][1000 genomes]
rs73358239	1.00[AMR][1000 genomes]
rs73358240	1.00[AMR][1000 genomes]
rs73358241	1.00[AMR][1000 genomes]
rs73358242	1.00[AMR][1000 genomes]
rs73358245	1.00[AMR][1000 genomes]
rs73358248	1.00[AMR][1000 genomes]
rs73358250	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053093	chr12:82645292-83287809	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv541551	chr12:82645292-83287809	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv899348	chr12:82744187-83169297	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv427917	chr12:82917031-83279712	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv521849	chr12:83013783-83991479	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv469490	chr12:83089431-83507269	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv559542	chr12:83089431-83507269	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	esv2758315	chr12:83101045-83357621	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv2759911	chr12:83101045-83357621	Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	esv2755991	chr12:83105631-83248605	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv469491	chr12:83108395-83203742	Enhancers Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv559543	chr12:83108395-83203742	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv2754173	chr12:83125000-83245838	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	esv2754509	chr12:83133090-83203742	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	esv999149	chr12:83137872-83206342	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83122000-83149000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr12:83138400-83151400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:83139800-83150200	Weak transcription	Fetal Lung	lung
4	chr12:83140400-83145000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr12:83140600-83148800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:83140600-83151200	Weak transcription	Fetal Heart	heart
7	chr12:83140800-83148600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr12:83140800-83150200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr12:83141000-83150200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:83141000-83154200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:83141400-83144800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:83142600-83148400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:83143000-83148800	Weak transcription	Brain Angular Gyrus	brain
14	chr12:83143400-83148600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:83143400-83148800	Weak transcription	Brain Substantia Nigra	brain
16	chr12:83143400-83149200	Weak transcription	Stomach Mucosa	stomach
17	chr12:83143600-83146600	Weak transcription	Brain Hippocampus Middle	brain
18	chr12:83144000-83144800	Weak transcription	Colon Smooth Muscle	Colon
19	chr12:83144000-83145000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:83144200-83144400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:83144200-83148600	Weak transcription	Primary monocytes fromperipheralblood	blood

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