Variant report

Variant	rs725490
Chromosome Location	chr2:20580860-20580861
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20549378..20551486-chr2:20579801..20582772,2	MCF-7	breast:
2	chr2:20550569..20551899-chr2:20580797..20581746,5	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	chr2:20579020..20581458-chr2:20591808..20594214,2	MCF-7	breast:
7	chr2:20578892..20581003-chr2:20669683..20672466,2	MCF-7	breast:
8	chr2:20565193..20568010-chr2:20578320..20581301,2	MCF-7	breast:
9	chr2:20544235..20547228-chr2:20579863..20582540,2	K562	blood:
10	chr2:20580053..20581963-chr2:20645867..20647441,2	MCF-7	breast:
11	chr2:20578802..20580924-chr2:20708669..20710555,2	MCF-7	breast:
12	chr2:20577324..20583172-chr2:20644517..20653341,20	MCF-7	breast:

No data

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

Extended variants
information (count: 8 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10209568	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1476941	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs343142	0.81[EUR][1000 genomes]
rs343161	0.87[ASN][1000 genomes]
rs4666386	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4666387	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6531236	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20575400-20581000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:20578200-20581200	Enhancers	Fetal Muscle Trunk	muscle
3	chr2:20579000-20581200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:20579000-20581200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:20579000-20581200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:20579200-20581200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr2:20579200-20581200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr2:20579200-20581200	Weak transcription	Liver	Liver
9	chr2:20579200-20581400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr2:20579200-20582400	Weak transcription	A549	lung
11	chr2:20579200-20582600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:20579200-20583000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:20579200-20583000	Weak transcription	HSMM	muscle
14	chr2:20579200-20583200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:20579200-20585400	Weak transcription	Colonic Mucosa	Colon
16	chr2:20579400-20581000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:20579400-20581000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:20579400-20581000	Weak transcription	Brain Anterior Caudate	brain
19	chr2:20579400-20581000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:20579400-20581000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr2:20579400-20581200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr2:20579400-20581200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr2:20579400-20581200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr2:20579400-20581200	Weak transcription	K562	blood
25	chr2:20579400-20581200	Weak transcription	NH-A	brain
26	chr2:20579400-20581200	Weak transcription	NHLF	lung
27	chr2:20579400-20581600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:20579400-20581800	Weak transcription	Fetal Brain Male	brain
29	chr2:20579400-20583000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:20579400-20584600	Weak transcription	Small Intestine	intestine
31	chr2:20579400-20585000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:20579400-20586000	Weak transcription	NHDF-Ad	bronchial
33	chr2:20579400-20586200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr2:20579400-20586200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:20579400-20586400	Weak transcription	Osteobl	bone
36	chr2:20579600-20581000	Weak transcription	Colon Smooth Muscle	Colon
37	chr2:20579600-20581000	Weak transcription	Fetal Heart	heart
38	chr2:20579600-20581200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:20579600-20581200	Weak transcription	Adipose Nuclei	Adipose
40	chr2:20579800-20581000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr2:20580200-20582000	Enhancers	Brain Substantia Nigra	brain
42	chr2:20580200-20582200	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr2:20580200-20582600	Enhancers	Brain Cingulate Gyrus	brain
44	chr2:20580400-20582000	Enhancers	Brain Hippocampus Middle	brain
45	chr2:20580400-20582800	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr2:20580400-20583200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:20580600-20581400	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr2:20580600-20581600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:20580600-20581800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:20580600-20581800	Enhancers	Brain Germinal Matrix	brain

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