Variant report

Variant	rs55853919
Chromosome Location	chr2:20581993-20581994
allele	G/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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 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	chr2:20567812..20569800-chr2:20580748..20582620,2	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	chr2:20544235..20547228-chr2:20579863..20582540,2	K562	blood:
8	chr2:20581393..20584603-chr2:20588898..20591026,3	MCF-7	breast:
9	chr2:20577324..20583172-chr2:20644517..20653341,20	MCF-7	breast:

No data

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

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10514649	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343162	0.81[ASN][1000 genomes]
rs62124614	0.87[AMR][1000 genomes]
rs62124615	0.87[AMR][1000 genomes]
rs62124616	0.87[AMR][1000 genomes];0.84[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:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20579200-20582400	Weak transcription	A549	lung
2	chr2:20579200-20582600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:20579200-20583000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:20579200-20583000	Weak transcription	HSMM	muscle
5	chr2:20579200-20583200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:20579200-20585400	Weak transcription	Colonic Mucosa	Colon
7	chr2:20579400-20583000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:20579400-20584600	Weak transcription	Small Intestine	intestine
9	chr2:20579400-20585000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:20579400-20586000	Weak transcription	NHDF-Ad	bronchial
11	chr2:20579400-20586200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:20579400-20586200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:20579400-20586400	Weak transcription	Osteobl	bone
14	chr2:20580200-20582000	Enhancers	Brain Substantia Nigra	brain
15	chr2:20580200-20582200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr2:20580200-20582600	Enhancers	Brain Cingulate Gyrus	brain
17	chr2:20580400-20582000	Enhancers	Brain Hippocampus Middle	brain
18	chr2:20580400-20582800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr2:20580400-20583200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:20580600-20582000	Enhancers	Fetal Intestine Small	intestine
21	chr2:20580600-20582200	Enhancers	Fetal Intestine Large	intestine
22	chr2:20580600-20582200	Enhancers	Fetal Muscle Leg	muscle
23	chr2:20581000-20582000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr2:20581000-20582600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:20581000-20582600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:20581000-20583400	Enhancers	HepG2	liver
27	chr2:20581200-20582000	Enhancers	Adipose Nuclei	Adipose
28	chr2:20581200-20582600	Enhancers	NHLF	lung
29	chr2:20581200-20583200	Enhancers	Duodenum Mucosa	Duodenum
30	chr2:20581200-20586200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr2:20581200-20586600	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr2:20581400-20585400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:20581600-20582400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr2:20581600-20583200	Weak transcription	K562	blood
35	chr2:20581600-20586200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:20581600-20586400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr2:20581600-20587400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:20581600-20601000	Weak transcription	Right Atrium	heart
39	chr2:20581800-20582000	Enhancers	Fetal Brain Male	brain
40	chr2:20581800-20583000	Weak transcription	Brain Angular Gyrus	brain
41	chr2:20581800-20583000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr2:20581800-20583000	Weak transcription	Fetal Lung	lung
43	chr2:20581800-20583200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr2:20581800-20583800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:20581800-20585000	Weak transcription	Placenta	Placenta
46	chr2:20581800-20586400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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