Variant report

Variant	rs17779542
Chromosome Location	chr19:52630913-52630914
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10405763	0.86[ASN][1000 genomes]
rs10405987	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10415918	0.89[ASN][1000 genomes]
rs10423034	0.90[ASN][1000 genomes]
rs11084145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12162225	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12459227	0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs12462872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12462908	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12609137	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12610551	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16983496	0.94[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs17835808	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3764537	0.97[GIH][hapmap]
rs45468391	0.89[ASN][1000 genomes]
rs4629085	0.87[CHB][hapmap]
rs8100114	0.88[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs8104987	0.97[GIH][hapmap]
rs8105609	0.94[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs8108125	0.94[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs8112502	0.94[CHB][hapmap];0.92[JPT][hapmap];0.91[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	esv34938	chr19:52227916-52630935	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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

No data

Chromatin state (count:114 , 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	chr19:52615800-52631400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
10	chr19:52616200-52631600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
11	chr19:52616200-52632600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
12	chr19:52616200-52634200	ZNF genes & repeats	Primary T cells from cord blood	blood
13	chr19:52616200-52640000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr19:52616200-52641200	ZNF genes & repeats	Dnd41	blood
15	chr19:52616200-52641400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:52616200-52641600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:52616400-52633000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
18	chr19:52616400-52641400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr19:52616800-52634000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
20	chr19:52617000-52640200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
21	chr19:52617200-52634000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
22	chr19:52617200-52640200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:52617400-52632000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
24	chr19:52617400-52632400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
25	chr19:52617400-52634200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr19:52617400-52641400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
27	chr19:52617800-52635600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
28	chr19:52618000-52640200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr19:52618400-52631000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
30	chr19:52618400-52631400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
31	chr19:52618400-52635000	ZNF genes & repeats	Fetal Intestine Large	intestine
32	chr19:52618600-52633600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
33	chr19:52619000-52631400	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
34	chr19:52620800-52634000	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr19:52624200-52631400	ZNF genes & repeats	Placenta	Placenta
36	chr19:52624200-52631600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
37	chr19:52624200-52634400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
38	chr19:52624200-52640200	ZNF genes & repeats	Fetal Intestine Small	intestine
39	chr19:52624400-52633000	ZNF genes & repeats	Ovary	ovary
40	chr19:52625000-52634200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:52625400-52635800	ZNF genes & repeats	Lung	lung
42	chr19:52625800-52631400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
43	chr19:52626200-52631000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
44	chr19:52626200-52631800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
45	chr19:52626400-52631200	ZNF genes & repeats	Brain Germinal Matrix	brain
46	chr19:52626600-52632000	Strong transcription	Brain Anterior Caudate	brain
47	chr19:52626600-52632000	ZNF genes & repeats	Colonic Mucosa	Colon
48	chr19:52626600-52634800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
49	chr19:52626600-52640400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr19:52627200-52640200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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