Variant report

Variant	rs28861172
Chromosome Location	chr19:21228956-21228957
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10402206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10406067	1.00[AMR][1000 genomes]
rs10406963	1.00[AMR][1000 genomes]
rs10407709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10409986	1.00[AMR][1000 genomes]
rs10410875	1.00[AMR][1000 genomes]
rs10413647	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10414113	1.00[AMR][1000 genomes]
rs10414275	1.00[AMR][1000 genomes]
rs10414637	1.00[AMR][1000 genomes]
rs10416560	1.00[AMR][1000 genomes]
rs10424510	1.00[AMR][1000 genomes]
rs10425744	1.00[AMR][1000 genomes]
rs10426896	1.00[AMR][1000 genomes]
rs11880192	1.00[AMR][1000 genomes]
rs11880228	1.00[AMR][1000 genomes]
rs12104385	1.00[AMR][1000 genomes]
rs13345915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28670574	1.00[AMR][1000 genomes]
rs28780501	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28840098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61734283	1.00[AMR][1000 genomes]
rs62122571	1.00[AMR][1000 genomes]
rs73531817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73546311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73548266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062776	chr19:20818886-21273361	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv932110	chr19:20818886-21278952	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	esv2763043	chr19:20818886-21290543	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	esv3385528	chr19:21030777-21495566	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv817536	chr19:21041855-21348237	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	esv1850387	chr19:21109758-21294264	Active TSS ZNF genes & repeats Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv911411	chr19:21184533-21263518	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv578949	chr19:21190572-21244049	ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
9	nsv960811	chr19:21200306-21371757	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21204200-21230400	Weak transcription	Gastric	stomach
2	chr19:21204400-21229200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr19:21204400-21231600	Weak transcription	Colonic Mucosa	Colon
4	chr19:21204400-21264800	Weak transcription	Right Ventricle	heart
5	chr19:21204600-21239800	Weak transcription	Colon Smooth Muscle	Colon
6	chr19:21206200-21241600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr19:21207200-21239400	Weak transcription	Hela-S3	cervix
8	chr19:21208600-21230000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr19:21209200-21235600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr19:21210200-21232200	Weak transcription	K562	blood
11	chr19:21211400-21235400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr19:21212000-21241400	Weak transcription	Fetal Heart	heart
13	chr19:21214000-21230200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr19:21216000-21229800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr19:21217400-21230200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr19:21217400-21230400	Weak transcription	NHEK	skin
17	chr19:21218800-21230400	Weak transcription	NHLF	lung
18	chr19:21220400-21235200	Weak transcription	NHDF-Ad	bronchial
19	chr19:21221400-21242000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:21222400-21230800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
21	chr19:21222400-21242200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr19:21223000-21244200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:21223200-21230000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr19:21223400-21230000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr19:21223400-21230200	Weak transcription	HSMMtube	muscle
26	chr19:21223400-21231400	Weak transcription	Placenta	Placenta
27	chr19:21223400-21235600	Weak transcription	NH-A	brain
28	chr19:21223600-21229800	Weak transcription	Osteobl	bone
29	chr19:21224000-21230800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:21224000-21230800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
31	chr19:21224000-21230800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
32	chr19:21224400-21230800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:21224400-21231000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
34	chr19:21224400-21232800	ZNF genes & repeats	Dnd41	blood
35	chr19:21224600-21230800	ZNF genes & repeats	Fetal Brain Female	brain
36	chr19:21224800-21230200	Weak transcription	Pancreas	Pancrea
37	chr19:21224800-21230800	ZNF genes & repeats	Primary T cells from cord blood	blood
38	chr19:21225000-21229200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr19:21225000-21229800	Weak transcription	Fetal Brain Male	brain
40	chr19:21225000-21230200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:21225000-21230400	Weak transcription	HSMM	muscle
42	chr19:21225200-21230800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
43	chr19:21225200-21234200	Weak transcription	A549	lung
44	chr19:21225400-21230400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr19:21225400-21230400	Weak transcription	Esophagus	oesophagus
46	chr19:21225400-21230800	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
47	chr19:21225600-21229400	Weak transcription	Fetal Thymus	thymus
48	chr19:21225600-21229600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr19:21225600-21229800	Weak transcription	Ovary	ovary
50	chr19:21225600-21230000	Weak transcription	Lung	lung

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