Variant report

Variant	rs12480381
Chromosome Location	chr20:53270297-53270298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:53263266..53270310-chr20:53278109..53284478,8	MCF-7	breast:
2	chr20:52821463..52842130-chr20:53255769..53272087,93	MCF-7	breast:
3	chr20:53268343..53271189-chr20:53272463..53275264,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11905815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11905874	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12479694	1.00[EUR][1000 genomes]
rs12479859	1.00[EUR][1000 genomes]
rs12480028	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12480040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12480981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12481217	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12481344	1.00[EUR][1000 genomes]
rs12481541	1.00[EUR][1000 genomes]
rs35234783	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6014109	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6014129	1.00[EUR][1000 genomes]
rs6023465	1.00[EUR][1000 genomes]
rs6023487	1.00[EUR][1000 genomes]
rs6023489	1.00[EUR][1000 genomes]
rs6023495	1.00[EUR][1000 genomes]
rs6023496	1.00[EUR][1000 genomes]
rs7266570	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73913649	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv1067497	chr20:53146241-53751820	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv1064144	chr20:53175264-53750137	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	nsv544302	chr20:53175264-53750137	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
5	nsv1060552	chr20:53234716-53655115	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53266200-53270800	Weak transcription	Ovary	ovary
2	chr20:53266800-53276000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr20:53267000-53270800	Weak transcription	Fetal Brain Female	brain
4	chr20:53267000-53277200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr20:53267200-53270800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr20:53267200-53270800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr20:53267200-53270800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr20:53267200-53270800	Weak transcription	Fetal Brain Male	brain
9	chr20:53267400-53270600	Weak transcription	Fetal Stomach	stomach
10	chr20:53268200-53270800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr20:53268200-53271000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr20:53269000-53270400	Weak transcription	Fetal Lung	lung

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