Variant report

Variant	rs11084149
Chromosome Location	chr19:52853439-52853440
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	chr19:52838795..52841074-chr19:52850925..52853608,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167554	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1120185	0.82[ASN][1000 genomes]
rs2251476	0.85[ASN][1000 genomes]
rs2560884	0.82[ASN][1000 genomes]
rs2560886	0.82[ASN][1000 genomes]
rs2560887	0.82[ASN][1000 genomes]
rs2560888	0.85[ASN][1000 genomes]
rs2560889	0.85[ASN][1000 genomes]
rs2560972	0.85[ASN][1000 genomes]
rs2560981	0.82[ASN][1000 genomes]
rs2560986	0.82[ASN][1000 genomes]
rs2657936	0.82[ASN][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:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52840400-52857400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:52840400-52865400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:52840600-52854800	Weak transcription	Gastric	stomach
4	chr19:52840600-52856800	Weak transcription	HSMM	muscle
5	chr19:52840600-52858800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr19:52840600-52861200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:52840800-52857000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr19:52840800-52857000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr19:52841400-52857000	Weak transcription	Right Ventricle	heart
10	chr19:52847200-52860000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr19:52848000-52862600	Weak transcription	Fetal Heart	heart
12	chr19:52848400-52870400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:52848800-52858400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr19:52849000-52854800	Weak transcription	Psoas Muscle	Psoas
15	chr19:52849000-52857000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr19:52849600-52853600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr19:52849600-52861400	ZNF genes & repeats	Fetal Intestine Small	intestine
18	chr19:52849800-52872200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:52850200-52853600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr19:52850200-52853800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr19:52850200-52854400	Strong transcription	Fetal Stomach	stomach
22	chr19:52850200-52855200	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr19:52850200-52856000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr19:52850400-52853600	Strong transcription	Dnd41	blood
25	chr19:52850400-52853800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr19:52850400-52854000	Strong transcription	Brain Substantia Nigra	brain
27	chr19:52850400-52855400	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr19:52850400-52862000	Strong transcription	Fetal Brain Female	brain
29	chr19:52850600-52855600	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr19:52850800-52853600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:52850800-52853600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
32	chr19:52850800-52853800	Strong transcription	Fetal Lung	lung
33	chr19:52850800-52854600	Weak transcription	Primary B cells from peripheral blood	blood
34	chr19:52850800-52854800	Strong transcription	Ovary	ovary
35	chr19:52850800-52855400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr19:52850800-52855400	Strong transcription	Brain Anterior Caudate	brain
37	chr19:52850800-52855800	Strong transcription	Brain Angular Gyrus	brain
38	chr19:52850800-52860600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr19:52850800-52861200	Strong transcription	Stomach Smooth Muscle	stomach
40	chr19:52850800-52870200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
41	chr19:52850800-52870200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr19:52851000-52853600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
43	chr19:52851000-52853600	Strong transcription	Adipose Nuclei	Adipose
44	chr19:52851000-52853600	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr19:52851000-52853800	Strong transcription	Fetal Muscle Leg	muscle
46	chr19:52851000-52854200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr19:52851000-52856000	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr19:52851000-52856400	Strong transcription	Brain Hippocampus Middle	brain
49	chr19:52851000-52857200	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr19:52851200-52854200	Strong transcription	Placenta	Placenta

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