Variant report

Variant	rs2616389
Chromosome Location	chr4:54511246-54511247
allele	C/T
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:
2	chr4:54510430..54512515-chr4:54515785..54518335,2	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];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1546527	0.96[ASN][1000 genomes]
rs2412470	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2572292	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2572300	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2590770	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2590771	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2590773	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2590778	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2590779	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2590809	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2590810	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2616383	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2616387	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2616388	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2616425	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2668522	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2668523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668525	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2668526	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2668527	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2668528	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2668550	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2668551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668552	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];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3113662	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs750545	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[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:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54507400-54511400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:54507400-54511600	Weak transcription	Right Ventricle	heart
3	chr4:54507800-54517000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr4:54507800-54520600	Weak transcription	Gastric	stomach
5	chr4:54508000-54512600	Weak transcription	Adipose Nuclei	Adipose
6	chr4:54508000-54519200	Weak transcription	Fetal Heart	heart
7	chr4:54509800-54512000	Enhancers	Fetal Intestine Large	intestine
8	chr4:54509800-54512200	Enhancers	Fetal Intestine Small	intestine
9	chr4:54509800-54513400	Enhancers	Pancreas	Pancrea
10	chr4:54510400-54511400	Weak transcription	Small Intestine	intestine
11	chr4:54510400-54511800	Enhancers	GM12878-XiMat	blood
12	chr4:54510400-54512000	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr4:54510400-54513400	Enhancers	Duodenum Mucosa	Duodenum
14	chr4:54510600-54511400	Enhancers	NHEK	skin
15	chr4:54510600-54511600	Enhancers	Liver	Liver
16	chr4:54510600-54511800	Enhancers	Placenta	Placenta
17	chr4:54510600-54511800	Enhancers	HMEC	breast
18	chr4:54510800-54511400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr4:54510800-54511400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:54510800-54511400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:54510800-54511400	Enhancers	Placenta Amnion	Placenta Amnion
22	chr4:54510800-54511400	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr4:54510800-54511600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:54510800-54511600	Enhancers	Left Ventricle	heart
25	chr4:54510800-54511600	Enhancers	Lung	lung
26	chr4:54510800-54511800	Enhancers	Right Atrium	heart
27	chr4:54510800-54512600	Enhancers	Psoas Muscle	Psoas
28	chr4:54511000-54511400	Weak transcription	Esophagus	oesophagus
29	chr4:54511000-54511400	Flanking Active TSS	Stomach Mucosa	stomach
30	chr4:54511000-54511600	Enhancers	Fetal Lung	lung
31	chr4:54511000-54512000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:54511000-54513600	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr4:54511200-54511400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
34	chr4:54511200-54511600	Enhancers	Colonic Mucosa	Colon

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