Variant report

Variant	rs1880563
Chromosome Location	chr19:37128075-37128076
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	chr19:37125356..37128254-chr19:37129692..37132005,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF461-3	chr19:37128059-37128185	l_1675_chr19:37069368-37128185_testes

Variant related genes	Relation type
ENSG00000197808	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs35481709	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73930863	1.00[EUR][1000 genomes]
rs8102705	0.87[YRI][hapmap]
rs826976	1.00[EUR][1000 genomes]
rs826978	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised 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	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers 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 miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv833817	chr19:36978852-37195695	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription 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 miRNA target site	73 gene(s)	inside rSNPs	diseases
7	esv3492171	chr19:37122012-37190210	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
8	esv3492172	chr19:37122562-37190060	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
9	esv3492173	chr19:37122562-37190060	Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37098000-37156000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:37102200-37135200	ZNF genes & repeats	Fetal Brain Female	brain
3	chr19:37106800-37151000	ZNF genes & repeats	Adipose Nuclei	Adipose
4	chr19:37106800-37156200	ZNF genes & repeats	Liver	Liver
5	chr19:37107000-37134800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr19:37107000-37152400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
7	chr19:37107800-37134600	ZNF genes & repeats	Brain Anterior Caudate	brain
8	chr19:37110400-37152600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr19:37115400-37131800	ZNF genes & repeats	Left Ventricle	heart
10	chr19:37117800-37128400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr19:37121400-37134600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
12	chr19:37121600-37135200	ZNF genes & repeats	Brain Hippocampus Middle	brain
13	chr19:37122600-37139800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
14	chr19:37122800-37134800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
15	chr19:37124600-37134600	ZNF genes & repeats	Brain Substantia Nigra	brain
16	chr19:37124800-37155600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
17	chr19:37125000-37134600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
18	chr19:37125000-37134600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
19	chr19:37126000-37128400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
20	chr19:37126000-37134600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
21	chr19:37126200-37134600	ZNF genes & repeats	Brain Cingulate Gyrus	brain
22	chr19:37126200-37156200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr19:37126400-37136200	ZNF genes & repeats	Brain Germinal Matrix	brain
24	chr19:37127000-37128600	ZNF genes & repeats	Lung	lung
25	chr19:37127000-37129800	ZNF genes & repeats	Fetal Stomach	stomach
26	chr19:37127000-37134400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
27	chr19:37127000-37140000	ZNF genes & repeats	Ovary	ovary
28	chr19:37127200-37128200	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
29	chr19:37127200-37131600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
30	chr19:37127200-37131600	ZNF genes & repeats	Colon Smooth Muscle	Colon
31	chr19:37127200-37134600	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
32	chr19:37127200-37134600	ZNF genes & repeats	A549	lung
33	chr19:37127200-37134800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr19:37127200-37141000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr19:37127200-37151000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr19:37127400-37132000	ZNF genes & repeats	Stomach Smooth Muscle	stomach
37	chr19:37127400-37135400	ZNF genes & repeats	Dnd41	blood
38	chr19:37127600-37128200	ZNF genes & repeats	Fetal Kidney	kidney
39	chr19:37127600-37128400	Weak transcription	Brain Angular Gyrus	brain
40	chr19:37127600-37128800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr19:37127600-37129400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr19:37127600-37129600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr19:37127600-37131600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr19:37127800-37129000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr19:37127800-37131600	ZNF genes & repeats	HSMM	muscle
46	chr19:37128000-37128800	Weak transcription	Fetal Lung	lung
47	chr19:37128000-37129600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr19:37128000-37134600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood

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