Variant report

Variant	rs6023419
Chromosome Location	chr20:53237968-53237969
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52824416..52826891-chr20:53237816..53240042,2	MCF-7	breast:
2	chr20:53236217..53238564-chr20:53241682..53243787,2	MCF-7	breast:
3	chr20:52824772..52826427-chr20:53237648..53240107,2	MCF-7	breast:
4	chr20:53227273..53231686-chr20:53235441..53239585,4	MCF-7	breast:
5	chr20:53115159..53116675-chr20:53236441..53239350,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs17000055	1.00[AMR][1000 genomes]
rs6014086	0.88[AFR][1000 genomes]
rs6023416	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6023417	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6023433	1.00[AMR][1000 genomes]
rs6512980	1.00[AMR][1000 genomes]
rs6512981	1.00[AMR][1000 genomes]
rs7274926	1.00[AMR][1000 genomes]
rs8114817	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv586282	chr20:53218978-53254815	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	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:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53204600-53240600	Weak transcription	Left Ventricle	heart
2	chr20:53217400-53240600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr20:53221600-53239000	Weak transcription	Osteobl	bone
4	chr20:53227800-53239000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr20:53229200-53240600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr20:53234800-53238200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr20:53235000-53241600	Enhancers	Fetal Brain Male	brain
8	chr20:53235200-53250400	Weak transcription	Psoas Muscle	Psoas
9	chr20:53236000-53238000	Enhancers	Fetal Brain Female	brain
10	chr20:53236000-53238800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr20:53236000-53241800	Weak transcription	Pancreas	Pancrea
12	chr20:53236200-53238400	Weak transcription	Brain Germinal Matrix	brain
13	chr20:53236200-53238400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr20:53236200-53238400	Weak transcription	Fetal Muscle Leg	muscle
15	chr20:53236200-53238600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr20:53236200-53240600	Weak transcription	Right Atrium	heart
17	chr20:53236200-53240800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr20:53236200-53250400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr20:53236400-53240600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr20:53236600-53238600	Weak transcription	Brain Anterior Caudate	brain
21	chr20:53236600-53238800	Weak transcription	Fetal Heart	heart
22	chr20:53236600-53239000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr20:53236600-53239000	Weak transcription	HSMMtube	muscle
24	chr20:53237400-53238000	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr20:53237800-53239000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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