Variant report

Variant	rs62186872
Chromosome Location	chr20:1398821-1398822
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1397917..1400734-chr20:1402889..1405956,3	K562	blood:
2	chr20:1397101..1400734-chr20:1402092..1406050,4	K562	blood:
3	chr20:1396772..1399275-chr20:1445760..1448572,2	MCF-7	breast:
4	chr20:1372764..1374884-chr20:1397366..1399828,3	MCF-7	breast:
5	chr20:1309378..1311616-chr20:1396285..1399669,3	MCF-7	breast:
6	chr20:1397834..1399758-chr20:1450418..1453215,2	K562	blood:

Variant related genes	Relation type
ENSG00000125775	Chromatin interaction
ENSG00000088832	Chromatin interaction
ENSG00000088833	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs2207831	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2224148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6074603	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6074608	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6074609	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6074625	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6079018	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6079040	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6079044	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6079045	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6079053	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6079055	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6079082	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62186873	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7270038	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7271175	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7353854	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv432095	chr20:1382500-1420340	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv1817885	chr20:1386940-1400227	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv1818242	chr20:1389773-1400227	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv1843659	chr20:1389773-1400227	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv1843922	chr20:1389773-1400227	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv1850632	chr20:1393861-1465597	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1395600-1399600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr20:1395600-1399800	Enhancers	NHLF	lung
3	chr20:1395600-1400000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr20:1395600-1400000	Enhancers	NHDF-Ad	bronchial
5	chr20:1395600-1400200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr20:1396200-1399600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr20:1396400-1399400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr20:1396400-1399600	Enhancers	NH-A	brain
9	chr20:1396400-1400000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr20:1396400-1400000	Enhancers	Placenta	Placenta
11	chr20:1396400-1400000	Enhancers	HUVEC	blood vessel
12	chr20:1396400-1400000	Enhancers	Osteobl	bone
13	chr20:1396600-1399400	Enhancers	Placenta Amnion	Placenta Amnion
14	chr20:1396600-1400000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr20:1396800-1400000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr20:1397000-1399200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr20:1397000-1400000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr20:1397200-1399000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr20:1398000-1399200	Enhancers	Spleen	Spleen
20	chr20:1398000-1399800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr20:1398000-1400000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr20:1398000-1400000	Enhancers	HMEC	breast
23	chr20:1398400-1399000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr20:1398400-1399600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr20:1398400-1399600	Flanking Active TSS	NHEK	skin
26	chr20:1398600-1399200	Enhancers	Muscle Satellite Cultured Cells	--
27	chr20:1398600-1400000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr20:1398800-1399000	Bivalent Enhancer	Fetal Muscle Leg	muscle
29	chr20:1398800-1399200	Enhancers	Cortex derived primary cultured neurospheres	brain

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