Variant report

Variant	rs66473405
Chromosome Location	chr15:56288527-56288528
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:56287606-56289839	K562	blood:	n/a	n/a
2	POLR2A	chr15:56288519-56288777	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:56285985..56288747-chr15:56326549..56330061,4	MCF-7	breast:
2	chr15:56284668..56287599-chr15:56288074..56291098,3	K562	blood:
3	chr15:56281891..56284127-chr15:56288031..56290159,2	K562	blood:
4	chr15:56288413..56291274-chr15:56330655..56333525,2	MCF-7	breast:

Variant related genes	Relation type
NEDD4	TF binding region
ENSG00000069869	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12439899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12593195	0.94[ASN][1000 genomes]
rs12901802	0.83[EUR][1000 genomes]
rs12902173	0.83[EUR][1000 genomes]
rs12904236	0.83[EUR][1000 genomes]
rs1472945	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34162982	0.83[EUR][1000 genomes]
rs34652186	0.83[EUR][1000 genomes]
rs35086304	0.83[EUR][1000 genomes]
rs35485562	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36045756	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4296197	0.83[EUR][1000 genomes]
rs66677855	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71476753	0.83[EUR][1000 genomes]
rs71476755	0.83[EUR][1000 genomes]
rs71476760	0.83[EUR][1000 genomes]
rs71476766	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167717	0.98[ASN][1000 genomes]
rs7182037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72732231	1.00[AFR][1000 genomes]
rs72736415	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7494783	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8025686	0.94[ASN][1000 genomes]
rs8038204	0.83[EUR][1000 genomes]
rs8039617	0.83[EUR][1000 genomes]
rs8042074	0.83[EUR][1000 genomes]
rs8042216	0.83[EUR][1000 genomes]
rs8043427	0.83[EUR][1000 genomes]
rs906811	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761872	chr15:56211065-56426501	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv904245	chr15:56229760-56324451	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv457159	chr15:56255774-56321854	Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv569543	chr15:56255774-56321854	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv457160	chr15:56273446-56320235	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
6	nsv569544	chr15:56273446-56320235	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
7	nsv457161	chr15:56274443-56324451	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a
8	nsv569545	chr15:56274443-56324451	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a
9	nsv569546	chr15:56274443-56337527	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56286600-56289200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:56286600-56289200	Weak transcription	Left Ventricle	heart
3	chr15:56286600-56292000	Weak transcription	Esophagus	oesophagus
4	chr15:56286800-56289000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr15:56286800-56290400	Weak transcription	Psoas Muscle	Psoas
6	chr15:56287000-56289400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr15:56287000-56291600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr15:56287000-56291800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr15:56287200-56289000	Weak transcription	HMEC	breast
10	chr15:56287200-56290200	Weak transcription	Fetal Intestine Large	intestine
11	chr15:56287200-56290400	Weak transcription	Placenta	Placenta
12	chr15:56287400-56288800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr15:56287400-56289000	Enhancers	NHEK	skin
14	chr15:56287400-56291600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:56287600-56291800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr15:56288000-56291600	Weak transcription	A549	lung
17	chr15:56288400-56291800	Enhancers	Hela-S3	cervix

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