Variant report

Variant	rs10420812
Chromosome Location	chr19:52867400-52867401
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	chr19:52861409..52864151-chr19:52865571..52868442,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10401299	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10406085	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10412822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10418954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10420125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10423371	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10423818	1.00[AMR][1000 genomes]
rs10424465	0.88[AFR][1000 genomes]
rs2560886	0.96[AFR][1000 genomes]
rs2560986	0.96[AFR][1000 genomes]
rs60323875	1.00[AMR][1000 genomes]
rs73581108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73581129	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers 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	24 gene(s)	inside rSNPs	diseases
6	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	esv3401193	chr19:52818960-52909749	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv912300	chr19:52832830-52928039	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv912301	chr19:52835210-52914233	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv912302	chr19:52859828-52928039	Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS 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	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52848400-52870400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:52849800-52872200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:52850800-52870200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
4	chr19:52850800-52870200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:52856800-52870200	ZNF genes & repeats	Ovary	ovary
6	chr19:52858800-52871800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:52859600-52868800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr19:52859800-52868200	Weak transcription	Right Ventricle	heart
9	chr19:52861800-52872200	ZNF genes & repeats	Fetal Lung	lung
10	chr19:52862000-52870200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
11	chr19:52862000-52871000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
12	chr19:52862000-52871000	ZNF genes & repeats	Fetal Brain Female	brain
13	chr19:52862000-52871200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr19:52862600-52871400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:52862800-52870600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
16	chr19:52863000-52868600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr19:52864000-52867800	Weak transcription	Fetal Brain Male	brain
18	chr19:52864200-52870600	ZNF genes & repeats	Brain Germinal Matrix	brain
19	chr19:52865200-52870200	ZNF genes & repeats	Fetal Intestine Large	intestine
20	chr19:52865200-52871200	ZNF genes & repeats	Adipose Nuclei	Adipose
21	chr19:52865200-52875400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:52865600-52871200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr19:52865800-52867600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr19:52865800-52867800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr19:52866000-52871200	ZNF genes & repeats	Dnd41	blood
26	chr19:52866400-52870400	ZNF genes & repeats	Brain Hippocampus Middle	brain
27	chr19:52866600-52868200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr19:52866600-52870200	ZNF genes & repeats	Brain Cingulate Gyrus	brain
29	chr19:52866600-52870200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
30	chr19:52866600-52872200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr19:52866600-52875400	ZNF genes & repeats	Liver	Liver
32	chr19:52866800-52867400	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
33	chr19:52866800-52867400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
34	chr19:52866800-52867400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
35	chr19:52866800-52867800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr19:52866800-52867800	Weak transcription	Left Ventricle	heart
37	chr19:52866800-52869800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
38	chr19:52866800-52870200	ZNF genes & repeats	Brain Anterior Caudate	brain
39	chr19:52866800-52871200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
40	chr19:52866800-52871200	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr19:52867000-52867400	ZNF genes & repeats	Stomach Smooth Muscle	stomach
42	chr19:52867000-52867800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr19:52867200-52868400	Weak transcription	Brain Substantia Nigra	brain
44	chr19:52867200-52868600	Weak transcription	Brain Angular Gyrus	brain
45	chr19:52867200-52868600	Weak transcription	Fetal Heart	heart
46	chr19:52867200-52872400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
47	chr19:52867400-52868400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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