Variant report

Variant	rs28659803
Chromosome Location	chr5:43166875-43166876
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:43161636..43163915-chr5:43165871..43168489,2	MCF-7	breast:
2	chr5:43166049..43168285-chr5:43170881..43173519,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172262	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1001718	1.00[AMR][1000 genomes]
rs10070393	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3849700	1.00[AMR][1000 genomes]
rs55730625	1.00[AMR][1000 genomes]
rs60384612	1.00[AMR][1000 genomes]
rs6859504	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6860747	1.00[AMR][1000 genomes]
rs6864556	1.00[AMR][1000 genomes]
rs6869639	1.00[AMR][1000 genomes]
rs6875245	1.00[AMR][1000 genomes]
rs6877778	1.00[AMR][1000 genomes]
rs6879509	1.00[AMR][1000 genomes]
rs6881357	1.00[AMR][1000 genomes]
rs6886169	1.00[AMR][1000 genomes]
rs6887110	1.00[AMR][1000 genomes]
rs6891509	1.00[AMR][1000 genomes]
rs6895975	1.00[AMR][1000 genomes]
rs6897663	1.00[AMR][1000 genomes]
rs73754524	1.00[AMR][1000 genomes]
rs73754532	1.00[AMR][1000 genomes]
rs747118	1.00[AMR][1000 genomes]
rs747119	1.00[AMR][1000 genomes]
rs7703982	1.00[AMR][1000 genomes]
rs7710205	1.00[AMR][1000 genomes]
rs7717370	1.00[AMR][1000 genomes]
rs7737740	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
7	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
8	nsv830274	chr5:43095551-43226087	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	138 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43122800-43174200	Weak transcription	Colonic Mucosa	Colon
2	chr5:43124000-43183000	Weak transcription	Small Intestine	intestine
3	chr5:43127600-43178000	Strong transcription	Dnd41	blood
4	chr5:43143400-43178200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:43148400-43169800	Strong transcription	Hela-S3	cervix
6	chr5:43150600-43167400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:43155200-43177200	Weak transcription	Fetal Heart	heart
8	chr5:43155800-43176600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:43156000-43178200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:43156200-43174600	Weak transcription	Right Ventricle	heart
11	chr5:43156600-43191200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr5:43156800-43174200	Weak transcription	Gastric	stomach
13	chr5:43156800-43177600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:43157000-43173400	Weak transcription	Brain Substantia Nigra	brain
15	chr5:43157000-43178400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr5:43158800-43168400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr5:43160800-43170000	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr5:43161000-43168600	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr5:43161000-43170600	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr5:43161200-43168600	Strong transcription	Liver	Liver
21	chr5:43161200-43169000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:43161200-43169600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr5:43161400-43167000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr5:43161400-43168600	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr5:43161400-43168800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:43161400-43168800	Strong transcription	Primary B cells from peripheral blood	blood
27	chr5:43161400-43169000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr5:43161400-43169000	Strong transcription	Adipose Nuclei	Adipose
29	chr5:43161400-43169200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr5:43161400-43176800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr5:43161800-43169400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr5:43161800-43170400	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr5:43162000-43167600	Weak transcription	Aorta	Aorta
34	chr5:43162000-43167800	Weak transcription	Ovary	ovary
35	chr5:43162000-43173000	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr5:43162000-43173400	Weak transcription	HSMMtube	muscle
37	chr5:43162000-43174000	Weak transcription	NHLF	lung
38	chr5:43162000-43174600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:43162000-43174600	Weak transcription	Esophagus	oesophagus
40	chr5:43162000-43174600	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr5:43162000-43176600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr5:43162000-43191600	Weak transcription	Fetal Brain Male	brain
43	chr5:43162200-43167200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr5:43162200-43173400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr5:43162200-43173600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr5:43162400-43169000	Strong transcription	Thymus	Thymus
47	chr5:43162600-43174600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr5:43163000-43169600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr5:43163200-43168000	Strong transcription	NH-A	brain
50	chr5:43163200-43168800	Strong transcription	Fetal Thymus	thymus

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