Variant report

Variant	rs28673525
Chromosome Location	chr21:40362437-40362438
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40186694..40188983-chr21:40361841..40364418,2	MCF-7	breast:
2	chr21:40282115..40285286-chr21:40361301..40363666,3	MCF-7	breast:
3	21:40348344-40365490..21:40748850-40752541	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000182093	Chromatin interaction
ENSG00000227406	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2836806	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836807	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836808	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4817978	0.90[ASN][1000 genomes]
rs58301407	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60329156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60789326	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73364803	0.96[EUR][1000 genomes]
rs9976408	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9976856	0.90[EUR][1000 genomes]
rs9976927	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9978603	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9985005	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062425	chr21:40172471-40380976	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544442	chr21:40172471-40380976	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv587477	chr21:40228920-40512004	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40352400-40370000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr21:40354600-40364600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr21:40356000-40369400	Enhancers	Left Ventricle	heart
4	chr21:40356800-40362800	Enhancers	Right Atrium	heart
5	chr21:40356800-40363000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr21:40357400-40363000	Enhancers	NHDF-Ad	bronchial
7	chr21:40357400-40376400	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr21:40358000-40363000	Enhancers	NHLF	lung
9	chr21:40358400-40363000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr21:40358600-40362800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr21:40358600-40363000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr21:40358600-40363800	Enhancers	Dnd41	blood
13	chr21:40358800-40363800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr21:40359000-40363800	Enhancers	H1 Cell Line	embryonic stem cell
15	chr21:40359000-40365400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr21:40359200-40362800	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr21:40359400-40363800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr21:40359400-40365000	Enhancers	Placenta	Placenta
19	chr21:40359600-40364200	Enhancers	Fetal Intestine Small	intestine
20	chr21:40359800-40364400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr21:40359800-40368400	Enhancers	Fetal Heart	heart
22	chr21:40360000-40365000	Enhancers	Fetal Intestine Large	intestine
23	chr21:40360000-40369200	Enhancers	Fetal Lung	lung
24	chr21:40360000-40370000	Enhancers	Primary hematopoietic stem cells	blood
25	chr21:40360400-40364800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
26	chr21:40360400-40368600	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr21:40360600-40363000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr21:40360600-40363000	Enhancers	Colonic Mucosa	Colon
29	chr21:40360600-40363200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr21:40360800-40362800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr21:40360800-40362800	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr21:40360800-40369600	Enhancers	Fetal Thymus	thymus
33	chr21:40360800-40376600	Weak transcription	Gastric	stomach
34	chr21:40361000-40362800	Enhancers	Esophagus	oesophagus
35	chr21:40361000-40362800	Enhancers	Psoas Muscle	Psoas
36	chr21:40361000-40363000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr21:40361000-40364000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr21:40361000-40364800	Enhancers	Lung	lung
39	chr21:40361200-40362600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr21:40361200-40362600	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr21:40361200-40362800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr21:40361200-40363000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
43	chr21:40361200-40363000	Enhancers	HSMM	muscle
44	chr21:40361200-40363400	Enhancers	Fetal Muscle Trunk	muscle
45	chr21:40361200-40364800	Enhancers	HUVEC	blood vessel
46	chr21:40361400-40362600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
47	chr21:40361400-40362600	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
48	chr21:40361400-40362600	Enhancers	Aorta	Aorta
49	chr21:40361400-40362600	Bivalent Enhancer	Stomach Mucosa	stomach
50	chr21:40361400-40362800	Enhancers	HSMMtube	muscle

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