Variant report

Variant	rs12162225
Chromosome Location	chr19:52631767-52631768
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	chr19:52631129..52632683-chr19:52637585..52640220,2	MCF-7	breast:
2	chr19:52631135..52633164-chr19:52639000..52640822,2	K562	blood:

Variant related genes	Relation type
ENSG00000238630	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10405763	0.87[ASN][1000 genomes]
rs10405987	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10415918	0.86[ASN][1000 genomes]
rs10423034	0.87[ASN][1000 genomes]
rs11084145	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12462872	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12462908	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12609137	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12610551	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16983496	0.87[ASN][1000 genomes]
rs17779542	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17835808	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs45468391	0.86[ASN][1000 genomes]
rs8100114	0.86[ASN][1000 genomes]
rs8105609	0.88[ASN][1000 genomes]
rs8108125	0.87[ASN][1000 genomes]
rs8112502	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS 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 miRNA target site	48 gene(s)	inside rSNPs	diseases
3	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
4	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
5	esv3433050	chr19:52595705-52639973	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv960859	chr19:52631598-52633888	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52606800-52640200	ZNF genes & repeats	Liver	Liver
2	chr19:52607000-52634000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:52609800-52639000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:52609800-52640200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
5	chr19:52610600-52631800	ZNF genes & repeats	Adipose Nuclei	Adipose
6	chr19:52613600-52639000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:52615200-52640200	ZNF genes & repeats	Fetal Brain Female	brain
8	chr19:52615600-52640200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr19:52616200-52632600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
10	chr19:52616200-52634200	ZNF genes & repeats	Primary T cells from cord blood	blood
11	chr19:52616200-52640000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr19:52616200-52641200	ZNF genes & repeats	Dnd41	blood
13	chr19:52616200-52641400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr19:52616200-52641600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:52616400-52633000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
16	chr19:52616400-52641400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr19:52616800-52634000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
18	chr19:52617000-52640200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
19	chr19:52617200-52634000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
20	chr19:52617200-52640200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:52617400-52632000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
22	chr19:52617400-52632400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
23	chr19:52617400-52634200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr19:52617400-52641400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
25	chr19:52617800-52635600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
26	chr19:52618000-52640200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr19:52618400-52635000	ZNF genes & repeats	Fetal Intestine Large	intestine
28	chr19:52618600-52633600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
29	chr19:52620800-52634000	Strong transcription	Placenta Amnion	Placenta Amnion
30	chr19:52624200-52634400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
31	chr19:52624200-52640200	ZNF genes & repeats	Fetal Intestine Small	intestine
32	chr19:52624400-52633000	ZNF genes & repeats	Ovary	ovary
33	chr19:52625000-52634200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr19:52625400-52635800	ZNF genes & repeats	Lung	lung
35	chr19:52626200-52631800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
36	chr19:52626600-52632000	Strong transcription	Brain Anterior Caudate	brain
37	chr19:52626600-52632000	ZNF genes & repeats	Colonic Mucosa	Colon
38	chr19:52626600-52634800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
39	chr19:52626600-52640400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr19:52627200-52640200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr19:52628800-52639800	ZNF genes & repeats	Fetal Stomach	stomach
42	chr19:52628800-52641400	Weak transcription	Brain Substantia Nigra	brain
43	chr19:52629000-52641200	Weak transcription	Right Ventricle	heart
44	chr19:52629200-52632400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr19:52629200-52633000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr19:52629200-52633200	Weak transcription	Hela-S3	cervix
47	chr19:52629200-52640800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr19:52629400-52632400	Weak transcription	NHDF-Ad	bronchial
49	chr19:52629400-52633200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr19:52629400-52641200	Weak transcription	Colon Smooth Muscle	Colon

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