Variant report

Variant	rs55887007
Chromosome Location	chr19:56958920-56958921
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11670383	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11670940	0.92[EUR][1000 genomes]
rs11672348	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11672698	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11878971	0.91[EUR][1000 genomes]
rs11883053	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1344093	0.92[EUR][1000 genomes]
rs55634464	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55905716	1.00[EUR][1000 genomes]
rs56163051	1.00[EUR][1000 genomes]
rs56281826	1.00[EUR][1000 genomes]
rs56342533	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56790623	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56805916	0.85[AMR][1000 genomes]
rs60020666	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs60471512	0.85[AMR][1000 genomes]
rs61635147	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61740673	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61743722	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv580385	chr19:56918598-57072433	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv1057240	chr19:56919831-57153659	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv544097	chr19:56919831-57153659	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv580386	chr19:56924761-57072433	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv1055357	chr19:56933632-57190007	ZNF genes & repeats Strong transcription Active TSS Enhancers Weak 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	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56955200-56960000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr19:56955600-56959600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:56955800-56959600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr19:56957200-56962200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:56957200-56987400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:56957400-56960800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
7	chr19:56957400-56960800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr19:56957400-56960800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr19:56957400-56960800	ZNF genes & repeats	Brain Anterior Caudate	brain
10	chr19:56957400-56960800	ZNF genes & repeats	Brain Cingulate Gyrus	brain
11	chr19:56957400-56960800	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
12	chr19:56957400-56960800	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
13	chr19:56957400-56960800	ZNF genes & repeats	Stomach Smooth Muscle	stomach
14	chr19:56957400-56961600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
15	chr19:56957400-56961600	ZNF genes & repeats	Brain Angular Gyrus	brain
16	chr19:56957400-56961800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
17	chr19:56957400-56961800	ZNF genes & repeats	Brain Germinal Matrix	brain
18	chr19:56957400-56962000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr19:56957400-56962000	ZNF genes & repeats	Fetal Brain Female	brain
20	chr19:56957400-56963000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
21	chr19:56957400-56963000	ZNF genes & repeats	Fetal Brain Male	brain
22	chr19:56957400-56963000	ZNF genes & repeats	Fetal Kidney	kidney
23	chr19:56957400-56963200	ZNF genes & repeats	Fetal Lung	lung
24	chr19:56957400-56964000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:56957400-56964200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
26	chr19:56957400-56968000	ZNF genes & repeats	Brain Hippocampus Middle	brain
27	chr19:56957400-56974200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
28	chr19:56957400-56976800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
29	chr19:56957400-56985000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
30	chr19:56957400-56987400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
31	chr19:56957400-56987400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr19:56957600-56959000	ZNF genes & repeats	Psoas Muscle	Psoas
33	chr19:56957600-56960600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
34	chr19:56957600-56960600	ZNF genes & repeats	Primary T cells from cord blood	blood
35	chr19:56957600-56960800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
36	chr19:56957600-56961000	ZNF genes & repeats	Brain Substantia Nigra	brain
37	chr19:56957600-56961000	ZNF genes & repeats	Fetal Muscle Leg	muscle
38	chr19:56957600-56961200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
39	chr19:56957600-56961600	ZNF genes & repeats	Liver	Liver
40	chr19:56957600-56961600	ZNF genes & repeats	Colon Smooth Muscle	Colon
41	chr19:56957600-56962200	ZNF genes & repeats	Adipose Nuclei	Adipose
42	chr19:56957600-56962200	ZNF genes & repeats	Ovary	ovary
43	chr19:56957800-56961000	ZNF genes & repeats	Left Ventricle	heart
44	chr19:56957800-56961200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
45	chr19:56957800-56961600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr19:56957800-56961600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
47	chr19:56958000-56961000	ZNF genes & repeats	Aorta	Aorta
48	chr19:56958400-56959400	Weak transcription	Right Ventricle	heart
49	chr19:56958400-56959400	Weak transcription	Dnd41	blood
50	chr19:56958400-56959400	Weak transcription	HSMMtube	muscle

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