Variant report

Variant	rs28495374
Chromosome Location	chr4:87921708-87921709
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87853540..87856355-chr4:87919742..87922210,3	MCF-7	breast:
2	chr4:87918478..87926067-chr4:87926181..87931063,13	MCF-7	breast:
3	chr4:87853601..87856121-chr4:87920561..87922700,3	K562	blood:
4	chr4:87852916..87856061-chr4:87919493..87922700,3	K562	blood:

Variant related genes	Relation type
ENSG00000163633	Chromatin interaction
ENSG00000172493	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10003331	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10015544	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10022825	1.00[ASN][1000 genomes]
rs10032200	1.00[ASN][1000 genomes]
rs10050309	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1037813	1.00[ASN][1000 genomes]
rs12508231	1.00[ASN][1000 genomes]
rs13103234	1.00[ASN][1000 genomes]
rs13108043	1.00[ASN][1000 genomes]
rs13134084	1.00[ASN][1000 genomes]
rs17012304	1.00[ASN][1000 genomes]
rs17030453	1.00[ASN][1000 genomes]
rs17604937	1.00[ASN][1000 genomes]
rs17668731	1.00[ASN][1000 genomes]
rs17668952	1.00[ASN][1000 genomes]
rs17703261	1.00[ASN][1000 genomes]
rs2230858	1.00[ASN][1000 genomes]
rs28667805	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28791499	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35658582	1.00[ASN][1000 genomes]
rs366327	1.00[ASN][1000 genomes]
rs56656813	1.00[ASN][1000 genomes]
rs58478399	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62306540	1.00[ASN][1000 genomes]
rs71607404	1.00[ASN][1000 genomes]
rs72877916	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72877918	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer 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	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87872600-87926200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr4:87899200-87922800	Weak transcription	Osteobl	bone
3	chr4:87899200-87925800	Weak transcription	Hela-S3	cervix
4	chr4:87899200-87926600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr4:87900000-87924400	Weak transcription	NHEK	skin
6	chr4:87903200-87926200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr4:87904200-87926200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr4:87914200-87927400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:87916000-87926200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:87916200-87922800	Weak transcription	Lung	lung
11	chr4:87916200-87927200	Weak transcription	Esophagus	oesophagus
12	chr4:87916400-87926200	Weak transcription	Fetal Intestine Large	intestine
13	chr4:87916400-87927200	Weak transcription	Gastric	stomach
14	chr4:87917800-87921800	Enhancers	Primary B cells from peripheral blood	blood
15	chr4:87918000-87925400	Enhancers	Placenta	Placenta
16	chr4:87919000-87927000	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr4:87919200-87921800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:87919200-87922000	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr4:87919200-87922200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr4:87919200-87927400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr4:87919400-87923000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr4:87919400-87925400	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr4:87919600-87922200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:87919800-87922200	Enhancers	Colon Smooth Muscle	Colon
25	chr4:87919800-87923400	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr4:87920000-87922000	Enhancers	Duodenum Mucosa	Duodenum
27	chr4:87920000-87922400	Enhancers	Liver	Liver
28	chr4:87920000-87923000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr4:87920000-87923400	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr4:87920200-87922200	Enhancers	Fetal Lung	lung
31	chr4:87920200-87923600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr4:87920400-87922600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr4:87920600-87921800	Enhancers	Fetal Intestine Small	intestine
34	chr4:87920600-87921800	Enhancers	NHLF	lung
35	chr4:87920600-87922200	Enhancers	Adipose Nuclei	Adipose
36	chr4:87920600-87923000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr4:87920600-87926000	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr4:87920800-87922200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr4:87920800-87922200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr4:87920800-87923000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr4:87920800-87923000	Enhancers	Fetal Stomach	stomach
42	chr4:87920800-87926000	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr4:87920800-87926000	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr4:87920800-87926200	Weak transcription	Thymus	Thymus
45	chr4:87921000-87921800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:87921000-87921800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr4:87921000-87921800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:87921000-87922000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr4:87921000-87922000	Enhancers	Small Intestine	intestine
50	chr4:87921000-87922200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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