Variant report

Variant	rs58276474
Chromosome Location	chr19:52843591-52843592
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52839220..52840960-chr19:52842927..52847321,5	MCF-7	breast:
2	chr19:52841087..52844060-chr19:52845758..52847842,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167554	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs56214747	0.83[AMR][1000 genomes]
rs73934432	1.00[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	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	nsv458742	chr19:52808986-52866171	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
8	nsv580008	chr19:52808986-52866171	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
9	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
10	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
11	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

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52840400-52848200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:52840400-52857400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:52840400-52865400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr19:52840600-52847000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr19:52840600-52847000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr19:52840600-52847000	Weak transcription	Brain Anterior Caudate	brain
7	chr19:52840600-52847000	Weak transcription	Brain Substantia Nigra	brain
8	chr19:52840600-52847600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:52840600-52848400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr19:52840600-52850400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr19:52840600-52850800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr19:52840600-52850800	Weak transcription	Ovary	ovary
13	chr19:52840600-52851000	Weak transcription	Colon Smooth Muscle	Colon
14	chr19:52840600-52851000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr19:52840600-52851000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr19:52840600-52851200	Weak transcription	Placenta	Placenta
17	chr19:52840600-52851600	Weak transcription	Left Ventricle	heart
18	chr19:52840600-52853200	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr19:52840600-52854800	Weak transcription	Gastric	stomach
20	chr19:52840600-52856800	Weak transcription	HSMM	muscle
21	chr19:52840600-52858800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr19:52840600-52861200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr19:52840800-52844000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr19:52840800-52844000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr19:52840800-52844800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr19:52840800-52846000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:52840800-52850200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr19:52840800-52850400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr19:52840800-52850800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr19:52840800-52851000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr19:52840800-52851000	Weak transcription	Fetal Muscle Leg	muscle
32	chr19:52840800-52851200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr19:52840800-52851400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr19:52840800-52851600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr19:52840800-52857000	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr19:52840800-52857000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr19:52841000-52843800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr19:52841000-52843800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:52841000-52846800	Weak transcription	Brain Hippocampus Middle	brain
40	chr19:52841000-52848400	Weak transcription	Fetal Lung	lung
41	chr19:52841000-52850800	Weak transcription	Primary T cells from cord blood	blood
42	chr19:52841000-52850800	Weak transcription	Fetal Brain Male	brain
43	chr19:52841200-52844000	Strong transcription	Fetal Stomach	stomach
44	chr19:52841200-52850800	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr19:52841200-52850800	Weak transcription	Fetal Kidney	kidney
46	chr19:52841400-52846200	Weak transcription	Fetal Heart	heart
47	chr19:52841400-52848400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr19:52841400-52850200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr19:52841400-52857000	Weak transcription	Right Ventricle	heart
50	chr19:52841600-52844200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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