Variant report

Variant	rs28588830
Chromosome Location	chr4:106845258-106845259
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:106838533..106840692-chr4:106845001..106847456,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10032388	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11097903	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13134201	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28397037	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28408688	0.91[EUR][1000 genomes]
rs28453940	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28459481	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28480231	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28523884	0.89[EUR][1000 genomes]
rs28530644	0.91[EUR][1000 genomes]
rs28560134	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28597911	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28676291	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28680557	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28680976	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4571330	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4616758	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4627867	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4643812	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4699201	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4699203	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4699204	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4699205	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6826402	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6843517	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6855132	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73836924	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73836926	0.96[EUR][1000 genomes]
rs73836933	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73836935	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73836936	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7663474	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7672530	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9790337	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9990974	0.80[AMR][1000 genomes];0.91[EUR][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	nsv1014993	chr4:106796019-106980727	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106831600-106878200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr4:106837600-106867600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:106838000-106864400	Weak transcription	Small Intestine	intestine
4	chr4:106843200-106853800	Weak transcription	GM12878-XiMat	blood
5	chr4:106843400-106845400	Enhancers	Fetal Intestine Small	intestine
6	chr4:106843600-106888400	Weak transcription	Pancreas	Pancrea
7	chr4:106843800-106858200	Weak transcription	Lung	lung
8	chr4:106844000-106845400	Enhancers	Fetal Intestine Large	intestine
9	chr4:106844000-106845400	Enhancers	HSMMtube	muscle
10	chr4:106844000-106845800	Enhancers	Fetal Heart	heart
11	chr4:106844400-106845400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:106844600-106845400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr4:106844600-106845400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:106844600-106845400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:106844600-106845400	Enhancers	Muscle Satellite Cultured Cells	--
16	chr4:106844600-106845400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:106844600-106845800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:106844600-106845800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:106844600-106845800	Enhancers	Placenta Amnion	Placenta Amnion
20	chr4:106844600-106845800	Enhancers	NHEK	skin
21	chr4:106844800-106845400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:106844800-106845400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr4:106844800-106845400	Enhancers	Fetal Lung	lung
24	chr4:106844800-106845400	Enhancers	Psoas Muscle	Psoas
25	chr4:106844800-106845400	Enhancers	HSMM	muscle
26	chr4:106844800-106859400	Weak transcription	Aorta	Aorta
27	chr4:106845000-106845600	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr4:106845000-106846000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:106845000-106857800	Weak transcription	Fetal Muscle Leg	muscle
30	chr4:106845200-106850600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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