Variant report

Variant	rs10006278
Chromosome Location	chr4:593469-593470
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	chr4:592248..593892-chr4:670830..672378,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000215375	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10001451	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10010598	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10017347	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10017435	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10018607	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10020292	1.00[AMR][1000 genomes]
rs10023609	1.00[AMR][1000 genomes]
rs10023934	0.90[AFR][1000 genomes]
rs10024023	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10025758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10027392	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10028157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10028526	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10028537	1.00[AMR][1000 genomes]
rs10029924	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10030020	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10035021	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12331186	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28366852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28399001	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28413992	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28414606	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28436699	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28452973	0.92[AFR][1000 genomes]
rs28459140	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28477853	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28478159	1.00[AMR][1000 genomes]
rs28510278	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28510755	1.00[AMR][1000 genomes]
rs28527330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28531889	1.00[AMR][1000 genomes]
rs28538930	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28540058	1.00[AMR][1000 genomes]
rs28546458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28551514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28594284	1.00[AFR][1000 genomes]
rs28599551	0.95[AFR][1000 genomes]
rs28601829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28605120	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28615478	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28633819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28665728	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28671384	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28706206	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28709824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28754367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28818828	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28843467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28862677	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6827034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6835327	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6842140	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73056559	1.00[AMR][1000 genomes]
rs7655485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7665160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7671294	1.00[AMR][1000 genomes]
rs7680416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7689014	1.00[AMR][1000 genomes]
rs7696942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9990446	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9991058	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9994679	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9995112	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9996316	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9996400	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9998466	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9998594	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9998776	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9999833	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv2830422	chr4:72247-681939	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv532703	chr4:72447-614414	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv931097	chr4:72447-683874	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv532704	chr4:85040-628550	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
8	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
9	nsv878245	chr4:509178-694613	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
11	nsv878246	chr4:592507-696848	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 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	chr4:575600-596400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr4:584600-595800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:592800-596800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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