Variant report

Variant	rs12980022
Chromosome Location	chr19:56910989-56910990
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56902006..56908060-chr19:56909612..56917978,15	K562	blood:
2	chr19:56910743..56913203-chr19:56914097..56915659,2	K562	blood:

Variant related genes	Relation type
ENSG00000267454	Chromatin interaction
ENSG00000266631	Chromatin interaction
ENSG00000198440	Chromatin interaction
ENSG00000018869	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11878390	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12972251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34450526	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35421936	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36090893	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[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	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
2	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
5	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
7	nsv544096	chr19:56905651-56933455	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56905000-56913600	ZNF genes & repeats	Liver	Liver
2	chr19:56905400-56911000	Weak transcription	Stomach Mucosa	stomach
3	chr19:56905600-56914600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:56905800-56914400	Weak transcription	Fetal Heart	heart
5	chr19:56908000-56913600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr19:56908000-56913600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
7	chr19:56908000-56914800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:56908200-56911400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr19:56908200-56912400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
10	chr19:56908200-56913000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
11	chr19:56908200-56914600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:56908400-56911800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
13	chr19:56908400-56912000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr19:56908400-56912000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
15	chr19:56908400-56913600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:56908600-56911000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr19:56908600-56911600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
18	chr19:56908600-56912200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr19:56908600-56913400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
20	chr19:56908800-56911200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
21	chr19:56908800-56911200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
22	chr19:56908800-56911400	ZNF genes & repeats	Primary T cells from cord blood	blood
23	chr19:56908800-56911600	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
24	chr19:56908800-56911600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:56908800-56911600	Strong transcription	Brain Cingulate Gyrus	brain
26	chr19:56908800-56911600	Strong transcription	Brain Hippocampus Middle	brain
27	chr19:56908800-56912000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr19:56908800-56912000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr19:56908800-56913600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
30	chr19:56908800-56913600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
31	chr19:56909000-56911000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr19:56909000-56911000	Strong transcription	Stomach Smooth Muscle	stomach
33	chr19:56909000-56911000	ZNF genes & repeats	Spleen	Spleen
34	chr19:56909000-56911200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr19:56909000-56911200	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr19:56909000-56911200	ZNF genes & repeats	Fetal Intestine Small	intestine
37	chr19:56909000-56911400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr19:56909000-56911400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
39	chr19:56909000-56911600	ZNF genes & repeats	Fetal Muscle Leg	muscle
40	chr19:56909000-56911800	Strong transcription	Left Ventricle	heart
41	chr19:56909000-56912000	ZNF genes & repeats	Fetal Stomach	stomach
42	chr19:56909000-56912000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
43	chr19:56909000-56913600	ZNF genes & repeats	Primary B cells from cord blood	blood
44	chr19:56909200-56911000	ZNF genes & repeats	Ovary	ovary
45	chr19:56909200-56911400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
46	chr19:56909200-56911400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr19:56909200-56911600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
48	chr19:56909200-56912000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
49	chr19:56909200-56912000	ZNF genes & repeats	Fetal Lung	lung
50	chr19:56909200-56912200	Strong transcription	Skeletal Muscle Female	skeletal muscle

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