Variant report

Variant	rs28620528
Chromosome Location	chr4:87850830-87850831
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87849580..87851531-chr4:87852776..87855807,3	K562	blood:
2	chr4:87849906..87854060-chr4:87926447..87928832,4	MCF-7	breast:
3	chr4:87848034..87854001-chr4:87854592..87858265,8	MCF-7	breast:
4	chr4:75256432..75258701-chr4:87850229..87853020,2	K562	blood:
5	chr4:87849195..87851661-chr4:88027634..88030050,2	MCF-7	breast:
6	chr4:87845889..87863516-chr4:87925389..87935181,79	K562	blood:
7	chr4:87849244..87851531-chr4:87853008..87856022,4	K562	blood:

Variant related genes	Relation type
ENSG00000163633	Chromatin interaction
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10029698	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10034541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1075989	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12186239	0.90[EUR][1000 genomes]
rs13103212	0.86[EUR][1000 genomes]
rs13112444	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13114907	0.81[EUR][1000 genomes]
rs13117826	0.86[EUR][1000 genomes]
rs13131035	0.90[EUR][1000 genomes]
rs13131194	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13134746	0.86[EUR][1000 genomes]
rs13143520	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13147942	0.86[EUR][1000 genomes]
rs13151671	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13151797	0.87[EUR][1000 genomes]
rs13434404	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2705623	0.86[EUR][1000 genomes]
rs28407685	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28439108	0.86[EUR][1000 genomes]
rs28447475	0.86[EUR][1000 genomes]
rs28457189	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28458234	0.99[EUR][1000 genomes]
rs28502831	0.90[EUR][1000 genomes]
rs28594717	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28610346	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28629974	0.90[EUR][1000 genomes]
rs28661703	0.89[EUR][1000 genomes]
rs28664715	0.90[EUR][1000 genomes]
rs28706796	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28729679	0.86[EUR][1000 genomes]
rs28854225	0.90[EUR][1000 genomes]
rs28886889	0.90[EUR][1000 genomes]
rs34077745	0.90[AMR][1000 genomes]
rs34991149	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35480728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35667731	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36053558	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71605624	0.84[EUR][1000 genomes]
rs71605686	0.86[EUR][1000 genomes]
rs71605687	0.86[EUR][1000 genomes]
rs71605688	0.90[EUR][1000 genomes]
rs71605691	0.93[EUR][1000 genomes]
rs71605693	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7683045	0.86[EUR][1000 genomes]
rs9993812	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9999001	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1013308	chr4:87769694-87870168	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv508297	chr4:87778783-87868508	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87825800-87854800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr4:87825800-87854800	Weak transcription	Right Ventricle	heart
3	chr4:87825800-87855200	Weak transcription	Fetal Stomach	stomach
4	chr4:87826000-87852400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr4:87829800-87855000	Weak transcription	Aorta	Aorta
6	chr4:87830200-87855200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:87830400-87854600	Weak transcription	Brain Hippocampus Middle	brain
8	chr4:87831000-87855000	Weak transcription	Fetal Lung	lung
9	chr4:87831400-87854400	Weak transcription	Fetal Heart	heart
10	chr4:87831400-87854800	Weak transcription	Right Atrium	heart
11	chr4:87832200-87854800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr4:87837200-87854400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr4:87838400-87855000	Weak transcription	Colonic Mucosa	Colon
14	chr4:87840200-87852200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:87840200-87854800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr4:87842600-87855400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:87843800-87854600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:87844000-87854600	Weak transcription	Colon Smooth Muscle	Colon
19	chr4:87844000-87854800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr4:87844000-87854800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr4:87844000-87854800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr4:87844000-87855000	Weak transcription	Brain Substantia Nigra	brain
23	chr4:87844000-87855000	Weak transcription	Fetal Muscle Leg	muscle
24	chr4:87844400-87852200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:87845600-87854800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr4:87845800-87855200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:87846400-87852400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:87846400-87855400	Weak transcription	Gastric	stomach
29	chr4:87846600-87851400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr4:87846600-87854800	Weak transcription	Brain Anterior Caudate	brain
31	chr4:87847800-87852400	Weak transcription	Fetal Intestine Small	intestine
32	chr4:87848000-87855000	Weak transcription	HSMMtube	muscle
33	chr4:87849200-87854800	Weak transcription	HSMM	muscle
34	chr4:87849400-87855000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr4:87849400-87855200	Weak transcription	Thymus	Thymus
36	chr4:87849600-87851200	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr4:87849600-87852000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr4:87849600-87854800	Weak transcription	Fetal Intestine Large	intestine
39	chr4:87849600-87855000	Weak transcription	Adipose Nuclei	Adipose
40	chr4:87849600-87855000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr4:87849600-87855000	Weak transcription	Stomach Mucosa	stomach
42	chr4:87849600-87855400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr4:87849800-87851000	Weak transcription	Psoas Muscle	Psoas
44	chr4:87849800-87851200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr4:87849800-87851200	Enhancers	Hela-S3	cervix
46	chr4:87849800-87852200	Weak transcription	Fetal Thymus	thymus
47	chr4:87849800-87852200	Weak transcription	Left Ventricle	heart
48	chr4:87849800-87852200	Weak transcription	Pancreas	Pancrea
49	chr4:87849800-87854400	Weak transcription	Liver	Liver
50	chr4:87849800-87854600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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