Variant report

Variant	rs2590778
Chromosome Location	chr4:54516068-54516069
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54510430..54512515-chr4:54515785..54518335,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1022187	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11945428	0.85[CEU][hapmap]
rs1546527	0.98[ASN][1000 genomes]
rs2412470	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2572292	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2572300	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2590770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2590771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2590773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2590779	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2590809	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2590810	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2616383	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2616387	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2616388	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2616389	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2616425	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2668522	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2668523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2668525	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668526	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668527	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668528	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2668550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668551	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2668552	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2668567	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3113662	0.86[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs750545	0.86[AMR][1000 genomes];0.82[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:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54507800-54517000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr4:54507800-54520600	Weak transcription	Gastric	stomach
3	chr4:54508000-54519200	Weak transcription	Fetal Heart	heart
4	chr4:54511400-54517200	Weak transcription	NHEK	skin
5	chr4:54511400-54520600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:54511600-54517400	Weak transcription	Lung	lung
7	chr4:54511600-54518800	Weak transcription	Liver	Liver
8	chr4:54511800-54518400	Weak transcription	GM12878-XiMat	blood
9	chr4:54512000-54517400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:54512200-54517000	Weak transcription	Fetal Intestine Small	intestine
11	chr4:54512600-54518600	Weak transcription	Colonic Mucosa	Colon
12	chr4:54513400-54516200	Weak transcription	Pancreas	Pancrea
13	chr4:54513400-54519600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:54514000-54516800	Weak transcription	Small Intestine	intestine
15	chr4:54515600-54516600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr4:54515600-54516600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:54515600-54516600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:54515600-54518800	Enhancers	Esophagus	oesophagus
19	chr4:54515600-54522400	Enhancers	Stomach Mucosa	stomach
20	chr4:54515800-54516200	Enhancers	Placenta Amnion	Placenta Amnion
21	chr4:54515800-54516400	Enhancers	Fetal Intestine Large	intestine
22	chr4:54515800-54516400	Enhancers	Placenta	Placenta
23	chr4:54515800-54516600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:54515800-54517000	Enhancers	Duodenum Mucosa	Duodenum
25	chr4:54515800-54518600	Active TSS	Adipose Nuclei	Adipose
26	chr4:54515800-54518800	Active TSS	Psoas Muscle	Psoas
27	chr4:54515800-54518800	Active TSS	Right Atrium	heart
28	chr4:54515800-54520800	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr4:54515800-54521000	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr4:54516000-54518600	Active TSS	Right Ventricle	heart
31	chr4:54516000-54518800	Active TSS	Left Ventricle	heart

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