Variant report

Variant	rs59030024
Chromosome Location	chr4:87904100-87904101
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:87903434..87906161-chr4:87925773..87929001,3	MCF-7	breast:
2	chr4:87901956..87904801-chr4:87936057..87937824,2	K562	blood:

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11931688	0.88[EUR][1000 genomes]
rs11933026	0.88[EUR][1000 genomes]
rs11933097	0.88[EUR][1000 genomes]
rs11933302	0.88[EUR][1000 genomes]
rs11936587	0.88[EUR][1000 genomes]
rs17012279	0.88[EUR][1000 genomes]
rs28372291	0.88[EUR][1000 genomes]
rs28544381	0.88[EUR][1000 genomes]
rs56800179	0.89[EUR][1000 genomes]
rs57785643	1.00[EUR][1000 genomes]
rs58016426	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59188173	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59830245	0.88[EUR][1000 genomes]
rs61009470	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6821413	1.00[EUR][1000 genomes]
rs6822432	1.00[EUR][1000 genomes]
rs6824639	0.88[EUR][1000 genomes]
rs6834549	1.00[EUR][1000 genomes]
rs6851332	0.88[EUR][1000 genomes]
rs6855627	1.00[EUR][1000 genomes]
rs7659244	0.88[EUR][1000 genomes]
rs7680465	0.88[EUR][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:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87872600-87926200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr4:87882600-87920200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:87882800-87912400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:87892200-87907000	Weak transcription	Brain Anterior Caudate	brain
5	chr4:87892400-87920600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr4:87892800-87909400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr4:87894400-87911000	Weak transcription	Pancreas	Pancrea
8	chr4:87894600-87904200	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr4:87894600-87915600	Weak transcription	Lung	lung
10	chr4:87894600-87921000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr4:87895200-87909400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr4:87895400-87920000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr4:87896200-87916000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr4:87896200-87919200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr4:87896800-87918800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr4:87897600-87915600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr4:87898200-87915400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:87899000-87915400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr4:87899000-87915400	Weak transcription	Left Ventricle	heart
20	chr4:87899000-87920600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr4:87899000-87921200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr4:87899200-87905000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:87899200-87905400	Weak transcription	Colon Smooth Muscle	Colon
24	chr4:87899200-87911000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr4:87899200-87913200	Weak transcription	Liver	Liver
26	chr4:87899200-87920800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr4:87899200-87922800	Weak transcription	Osteobl	bone
28	chr4:87899200-87925800	Weak transcription	Hela-S3	cervix
29	chr4:87899200-87926600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:87900000-87915600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:87900000-87924400	Weak transcription	NHEK	skin
32	chr4:87900200-87908200	Weak transcription	Stomach Mucosa	stomach
33	chr4:87900200-87920800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:87901000-87913000	Weak transcription	Fetal Intestine Large	intestine
35	chr4:87901200-87913200	Weak transcription	HepG2	liver
36	chr4:87902200-87904400	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr4:87902400-87904400	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr4:87902600-87904200	Enhancers	Primary hematopoietic stem cells	blood
39	chr4:87902600-87904200	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr4:87902600-87904600	Enhancers	Primary B cells from peripheral blood	blood
41	chr4:87902800-87904400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr4:87903000-87904400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr4:87903000-87904600	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr4:87903000-87904600	Enhancers	Primary B cells from cord blood	blood
45	chr4:87903200-87918800	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr4:87903200-87926200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr4:87903400-87908400	Weak transcription	GM12878-XiMat	blood
48	chr4:87903400-87909600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr4:87903400-87915400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr4:87903600-87904400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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