Variant report

Variant	rs10423647
Chromosome Location	chr19:45001398-45001399
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	chr19:44997908..45002641-chr19:45002925..45005659,8	MCF-7	breast:
2	chr19:44999410..45002615-chr19:45002996..45005888,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF180-3	chr19:45001336-45001429	NONHSAT066701
2	lnc-ZNF180-3	chr19:45001336-45001429	NONHSAT066700
3	lnc-ZNF180-3	chr19:45001336-45001424	NONHSAT066702

Variant related genes	Relation type
ENSG00000167384	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10422951	1.00[TSI][hapmap]
rs11881569	0.85[ASW][hapmap];0.91[LWK][hapmap];0.82[MEX][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11883035	1.00[ASW][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12327834	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12327835	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16989313	1.00[EUR][1000 genomes]
rs57371815	1.00[EUR][1000 genomes]
rs73558071	1.00[EUR][1000 genomes]
rs73560018	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912112	chr19:44853707-45011727	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription 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 miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv912114	chr19:44858776-45002563	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1061350	chr19:44869075-45035469	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers 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	18 gene(s)	inside rSNPs	diseases
4	nsv521513	chr19:45000059-45002563	Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44978800-45003400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
2	chr19:44993600-45002000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr19:44993600-45002000	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
4	chr19:44993600-45003600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr19:44993600-45003600	ZNF genes & repeats	Primary B cells from cord blood	blood
6	chr19:44993600-45003600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
7	chr19:44993600-45003600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr19:44994000-45001800	ZNF genes & repeats	Dnd41	blood
9	chr19:44994000-45002200	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
10	chr19:44994000-45002200	ZNF genes & repeats	Brain Cingulate Gyrus	brain
11	chr19:44994000-45002600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
12	chr19:44994000-45002600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
13	chr19:44994000-45002800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
14	chr19:44994000-45002800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
15	chr19:44994000-45002800	ZNF genes & repeats	Brain Anterior Caudate	brain
16	chr19:44994000-45002800	ZNF genes & repeats	HepG2	liver
17	chr19:44994000-45003000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
18	chr19:44994000-45003000	ZNF genes & repeats	Fetal Brain Female	brain
19	chr19:44994000-45003000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
20	chr19:44994000-45003200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
21	chr19:44994000-45003200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
22	chr19:44994000-45003200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:44994000-45003200	ZNF genes & repeats	Liver	Liver
24	chr19:44994000-45003400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr19:44994000-45003400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:44994000-45003400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
27	chr19:44994000-45003600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
28	chr19:44994000-45003600	ZNF genes & repeats	GM12878-XiMat	blood
29	chr19:44994000-45003800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:44994000-45003800	ZNF genes & repeats	Brain Germinal Matrix	brain
31	chr19:44994200-45002000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr19:44994200-45002200	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr19:44994200-45002600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
34	chr19:44994200-45002600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
35	chr19:44994200-45002800	ZNF genes & repeats	Adipose Nuclei	Adipose
36	chr19:44994200-45002800	ZNF genes & repeats	Brain Substantia Nigra	brain
37	chr19:44994200-45003000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr19:44994200-45003000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
39	chr19:44994200-45003000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
40	chr19:44994200-45003000	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
41	chr19:44994200-45003000	ZNF genes & repeats	Brain Hippocampus Middle	brain
42	chr19:44994200-45003000	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
43	chr19:44994200-45003000	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
44	chr19:44994200-45003200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
45	chr19:44994200-45003200	ZNF genes & repeats	Ovary	ovary
46	chr19:44994200-45003200	ZNF genes & repeats	Rectal Smooth Muscle	rectum
47	chr19:44994200-45003400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
48	chr19:44994200-45003400	ZNF genes & repeats	Fetal Intestine Large	intestine
49	chr19:44994200-45003400	ZNF genes & repeats	Fetal Lung	lung
50	chr19:44994200-45003600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung

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