Variant report

Variant	rs62124611
Chromosome Location	chr2:20582683-20582684
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20549378..20551486-chr2:20579801..20582772,2	MCF-7	breast:
2	chr2:20578207..20580776-chr2:20580974..20582727,2	MCF-7	breast:
3	chr2:20577593..20583526-chr2:20584013..20588692,7	MCF-7	breast:
4	chr2:20582061..20584787-chr2:20647277..20649666,2	MCF-7	breast:
5	chr2:20573304..20576530-chr2:20577907..20583085,5	MCF-7	breast:
6	chr2:20581268..20583206-chr2:20830863..20833030,2	MCF-7	breast:
7	chr2:20581393..20584603-chr2:20588898..20591026,3	MCF-7	breast:
8	chr2:20577324..20583172-chr2:20644517..20653341,20	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000055917	Chromatin interaction
ENSG00000232800	Chromatin interaction
ENSG00000143878	Chromatin interaction
ENSG00000228950	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10856798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11096661	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11096662	0.85[AMR][1000 genomes]
rs11675693	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11678068	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11683057	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11692468	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11692578	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11887662	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12472111	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12472980	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12475795	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17653822	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17670898	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2098293	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35133647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58495411	0.87[AMR][1000 genomes]
rs62124613	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62124635	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72788926	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72788927	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873716	chr2:20572094-20621404	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv581165	chr2:20581058-20616990	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20579200-20583000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:20579200-20583000	Weak transcription	HSMM	muscle
3	chr2:20579200-20583200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:20579200-20585400	Weak transcription	Colonic Mucosa	Colon
5	chr2:20579400-20583000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:20579400-20584600	Weak transcription	Small Intestine	intestine
7	chr2:20579400-20585000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:20579400-20586000	Weak transcription	NHDF-Ad	bronchial
9	chr2:20579400-20586200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:20579400-20586200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:20579400-20586400	Weak transcription	Osteobl	bone
12	chr2:20580400-20582800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr2:20580400-20583200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:20581000-20583400	Enhancers	HepG2	liver
15	chr2:20581200-20583200	Enhancers	Duodenum Mucosa	Duodenum
16	chr2:20581200-20586200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr2:20581200-20586600	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr2:20581400-20585400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:20581600-20583200	Weak transcription	K562	blood
20	chr2:20581600-20586200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:20581600-20586400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr2:20581600-20587400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:20581600-20601000	Weak transcription	Right Atrium	heart
24	chr2:20581800-20583000	Weak transcription	Brain Angular Gyrus	brain
25	chr2:20581800-20583000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr2:20581800-20583000	Weak transcription	Fetal Lung	lung
27	chr2:20581800-20583200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr2:20581800-20583800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:20581800-20585000	Weak transcription	Placenta	Placenta
30	chr2:20581800-20586400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:20582000-20583000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr2:20582000-20584200	Weak transcription	Fetal Intestine Small	intestine
33	chr2:20582200-20584600	Weak transcription	Fetal Intestine Large	intestine
34	chr2:20582400-20583200	Enhancers	A549	lung
35	chr2:20582400-20583400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:20582400-20584000	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr2:20582600-20583400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:20582600-20586000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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