Variant report

Variant	rs6023396
Chromosome Location	chr20:53215784-53215785
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:53213011..53216451-chr20:53226919..53231866,4	MCF-7	breast:
2	chr20:53212556..53214088-chr20:53214939..53217092,2	MCF-7	breast:
3	chr17:56708434..56710968-chr20:53214691..53216533,3	MCF-7	breast:
4	chr20:53201780..53208417-chr20:53214130..53221252,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212195	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10485784	0.84[EUR][1000 genomes]
rs13433172	0.86[AMR][1000 genomes]
rs17327539	0.84[EUR][1000 genomes]
rs55705559	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55960128	0.84[EUR][1000 genomes]
rs56138015	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56294816	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56371656	0.86[EUR][1000 genomes]
rs58298733	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6014078	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6014080	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6014087	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6014089	0.83[AMR][1000 genomes]
rs6023382	0.86[EUR][1000 genomes]
rs6023383	0.86[EUR][1000 genomes]
rs6023394	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6023397	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6023398	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6023401	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6023403	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6023422	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6091933	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6098093	0.83[EUR][1000 genomes]
rs6098099	0.84[EUR][1000 genomes]
rs6098103	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6098104	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6098105	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6098111	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6098116	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6098118	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6098123	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67907005	0.84[EUR][1000 genomes]
rs7269966	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73140147	0.84[EUR][1000 genomes]
rs73144063	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73144072	0.96[EUR][1000 genomes]
rs73144079	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73144086	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73146053	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73146055	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53202200-53230800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr20:53204600-53240600	Weak transcription	Left Ventricle	heart
3	chr20:53206400-53226600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr20:53206600-53216600	Weak transcription	Fetal Brain Female	brain
5	chr20:53207200-53217000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr20:53209000-53216600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr20:53209800-53216200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr20:53210800-53216200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr20:53213200-53217000	Weak transcription	Psoas Muscle	Psoas
10	chr20:53215000-53217400	Weak transcription	Fetal Brain Male	brain
11	chr20:53215200-53217000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr20:53215200-53236400	Weak transcription	Aorta	Aorta
13	chr20:53215400-53216400	Weak transcription	Brain Germinal Matrix	brain
14	chr20:53215600-53216400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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