Variant report

Variant	rs2668552
Chromosome Location	chr4:54510427-54510428
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54457408..54459119-chr4:54508678..54511662,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000072201	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1022187	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1546527	0.96[ASN][1000 genomes]
rs2412470	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2572292	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2572300	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2590770	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2590771	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2590773	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2590778	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2590779	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2590809	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2590810	0.94[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2616383	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2616387	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2616388	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2616389	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2616425	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2668522	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2668523	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668525	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2668526	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2668527	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2668528	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2668550	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2668551	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668567	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3113662	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs750545	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[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	nsv829936	chr4:54367783-54556123	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54501400-54510800	Weak transcription	Right Atrium	heart
2	chr4:54506800-54511000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr4:54507200-54510600	Weak transcription	Placenta	Placenta
4	chr4:54507200-54511000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:54507400-54510800	Weak transcription	Esophagus	oesophagus
6	chr4:54507400-54510800	Weak transcription	Left Ventricle	heart
7	chr4:54507400-54511400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:54507400-54511600	Weak transcription	Right Ventricle	heart
9	chr4:54507800-54510800	Weak transcription	Lung	lung
10	chr4:54507800-54510800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr4:54507800-54517000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr4:54507800-54520600	Weak transcription	Gastric	stomach
13	chr4:54508000-54511000	Weak transcription	Fetal Lung	lung
14	chr4:54508000-54512600	Weak transcription	Adipose Nuclei	Adipose
15	chr4:54508000-54519200	Weak transcription	Fetal Heart	heart
16	chr4:54509000-54511000	Enhancers	Stomach Mucosa	stomach
17	chr4:54509800-54512000	Enhancers	Fetal Intestine Large	intestine
18	chr4:54509800-54512200	Enhancers	Fetal Intestine Small	intestine
19	chr4:54509800-54513400	Enhancers	Pancreas	Pancrea
20	chr4:54510000-54511200	Weak transcription	Colonic Mucosa	Colon
21	chr4:54510200-54510600	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr4:54510400-54511400	Weak transcription	Small Intestine	intestine
23	chr4:54510400-54511800	Enhancers	GM12878-XiMat	blood
24	chr4:54510400-54512000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr4:54510400-54513400	Enhancers	Duodenum Mucosa	Duodenum

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