Variant report

Variant	rs2024578
Chromosome Location	chr20:53285374-53285375
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:53284416..53286265-chr3:64518639..64520757,22	MCF-7	breast:
2	chr20:46292698..46293246-chr20:53284814..53285656,2	MCF-7	breast:
3	chr20:53284372..53285796-chr3:64515862..64518059,16	MCF-7	breast:
4	chr17:62398118..62398967-chr20:53284782..53285787,4	MCF-7	breast:
5	chr20:53285185..53285713-chr3:64517860..64518552,2	MCF-7	breast:
6	chr20:53282910..53285557-chr7:133594422..133596091,2	MCF-7	breast:
7	chr20:53284944..53285815-chr3:64703842..64704565,3	MCF-7	breast:
8	chr20:53263133..53263665-chr20:53284817..53285627,3	MCF-7	breast:
9	chr20:52823269..52825288-chr20:53284524..53286083,2	MCF-7	breast:
10	chr20:53283455..53285734-chr3:64506182..64507970,2	MCF-7	breast:
11	chr20:53284783..53285767-chr20:53342880..53343689,2	MCF-7	breast:
12	chr20:53275084..53275860-chr20:53284526..53285663,3	MCF-7	breast:
13	chr20:53265683..53266760-chr20:53284578..53285846,10	MCF-7	breast:
14	chr20:53265522..53267786-chr20:53285191..53286958,2	MCF-7	breast:
15	chr20:53284841..53286002-chr20:53342966..53343740,4	MCF-7	breast:
16	chr20:52840058..52843007-chr20:53284448..53286480,2	MCF-7	breast:
17	chr20:53283718..53285867-chr3:64515756..64517189,9	MCF-7	breast:
18	chr20:53285227..53285747-chr3:64636577..64637535,2	MCF-7	breast:
19	chr20:53283717..53285430-chr3:64475712..64477407,2	MCF-7	breast:
20	chr20:53284827..53285806-chr20:53297032..53297616,3	MCF-7	breast:
21	chr20:52574355..52575313-chr20:53285096..53285689,2	MCF-7	breast:
22	chr20:53284753..53285783-chr3:64518725..64520000,8	MCF-7	breast:
23	chr20:53272079..53274152-chr20:53283538..53285655,2	MCF-7	breast:
24	chr20:52556243..52557049-chr20:53285071..53285677,3	MCF-7	breast:
25	chr20:53266056..53266639-chr20:53284797..53285724,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000163638	Chromatin interaction
ENSG00000236352	Chromatin interaction
ENSG00000101132	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1012644	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2904390	0.81[ASN][1000 genomes]
rs4811516	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6068933	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6068934	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6098145	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6123403	1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][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	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
2	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
3	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
4	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:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53281800-53285600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr20:53284200-53285600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr20:53284800-53285800	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr20:53285000-53285400	Enhancers	H1 Cell Line	embryonic stem cell
5	chr20:53285000-53285400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr20:53285000-53285600	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr20:53285000-53285600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
8	chr20:53285000-53285600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
9	chr20:53285000-53285600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr20:53285000-53285600	Enhancers	Fetal Heart	heart
11	chr20:53285000-53285600	Enhancers	Placenta	Placenta
12	chr20:53285000-53285600	Enhancers	Ovary	ovary
13	chr20:53285000-53285600	Enhancers	GM12878-XiMat	blood
14	chr20:53285000-53285800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr20:53285000-53285800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr20:53285000-53285800	Enhancers	Liver	Liver
17	chr20:53285000-53285800	Enhancers	Right Ventricle	heart
18	chr20:53285200-53285400	Enhancers	Colon Smooth Muscle	Colon
19	chr20:53285200-53285600	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr20:53285200-53285600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
21	chr20:53285200-53285600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr20:53285200-53285600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr20:53285200-53285600	Bivalent Enhancer	Fetal Stomach	stomach
24	chr20:53285200-53285600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
25	chr20:53285200-53285800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr20:53285200-53285800	Bivalent Enhancer	Fetal Muscle Leg	muscle
27	chr20:53285200-53285800	Enhancers	Spleen	Spleen
28	chr20:53285200-53285800	Enhancers	HepG2	liver

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