Variant report

Variant	rs189069
Chromosome Location	chr19:53496480-53496481
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53465058..53468377-chr19:53495533..53497921,4	K562	blood:

Variant related genes	Relation type
ENSG00000180257	Chromatin interaction
ENSG00000221874	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10403221	0.83[ASN][1000 genomes]
rs10426414	0.82[ASN][1000 genomes]
rs10426833	0.92[ASN][1000 genomes]
rs11880927	0.87[ASN][1000 genomes]
rs11881425	0.92[ASN][1000 genomes]
rs12463150	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12610330	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12610677	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1612464	0.87[ASN][1000 genomes]
rs1650936	0.86[ASN][1000 genomes]
rs1650937	0.86[ASN][1000 genomes]
rs1650938	0.87[ASN][1000 genomes]
rs1650940	0.89[ASN][1000 genomes]
rs1650941	0.89[ASN][1000 genomes]
rs1650944	0.88[ASN][1000 genomes]
rs1650947	0.88[ASN][1000 genomes]
rs1650948	0.85[ASN][1000 genomes]
rs1650949	0.92[ASN][1000 genomes]
rs1661907	0.87[ASN][1000 genomes]
rs1661908	0.94[ASN][1000 genomes]
rs1661911	0.89[ASN][1000 genomes]
rs1661912	0.89[ASN][1000 genomes]
rs1661917	0.88[ASN][1000 genomes]
rs1661918	0.94[ASN][1000 genomes]
rs1661947	0.86[ASN][1000 genomes]
rs16984291	0.88[ASN][1000 genomes]
rs16984293	0.89[ASN][1000 genomes]
rs2584263	0.94[ASN][1000 genomes]
rs2870437	0.97[ASN][1000 genomes]
rs329693	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57822302	0.94[ASN][1000 genomes]
rs59929172	0.92[ASN][1000 genomes]
rs60920143	0.89[ASN][1000 genomes]
rs6509713	0.88[ASN][1000 genomes]
rs7248038	0.94[ASN][1000 genomes]
rs7256272	0.92[ASN][1000 genomes]
rs7256944	0.94[ASN][1000 genomes]
rs73582974	0.92[ASN][1000 genomes]
rs8100426	0.87[ASN][1000 genomes]
rs8105271	0.85[ASN][1000 genomes]
rs8106463	0.95[ASN][1000 genomes]
rs8106476	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066762	chr19:53112568-53552217	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv432072	chr19:53144788-53554388	Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1067280	chr19:53193570-53567287	Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv544062	chr19:53193570-53567287	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv580030	chr19:53194344-53547394	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv530807	chr19:53210488-53695881	Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	esv3326632	chr19:53371248-53697569	Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	esv2758506	chr19:53410459-53652575	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	esv2758769	chr19:53410459-53652575	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
10	nsv428370	chr19:53410459-53652575	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
11	esv2757701	chr19:53470514-53554240	Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	esv34546	chr19:53478109-53509688	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv817861	chr19:53484032-53505860	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv458753	chr19:53485090-53552296	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	nsv458754	chr19:53485090-53552296	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
16	nsv580046	chr19:53485090-53552296	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 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	chr19:53494600-53498000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr19:53495200-53497400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:53495400-53496600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr19:53495400-53497400	ZNF genes & repeats	Liver	Liver
5	chr19:53495400-53497400	ZNF genes & repeats	Spleen	Spleen
6	chr19:53495400-53497600	Active TSS	NHLF	lung
7	chr19:53495600-53496800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:53495600-53497000	Active TSS	Primary T helper naive cells from peripheral blood	blood
9	chr19:53495600-53497000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr19:53495600-53497800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr19:53495800-53496600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
12	chr19:53495800-53496800	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr19:53495800-53496800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr19:53495800-53496800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
15	chr19:53495800-53496800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr19:53495800-53497200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr19:53495800-53497200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:53495800-53497200	Active TSS	Primary T killer memory cells from peripheral blood	blood
19	chr19:53495800-53497200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr19:53495800-53497400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:53495800-53497400	Active TSS	Brain Cingulate Gyrus	brain
22	chr19:53495800-53497400	Active TSS	Brain Substantia Nigra	brain
23	chr19:53495800-53497600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr19:53495800-53497600	Active TSS	Brain Angular Gyrus	brain
25	chr19:53495800-53497600	Active TSS	Brain Anterior Caudate	brain
26	chr19:53495800-53497600	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr19:53495800-53497600	Active TSS	Rectal Smooth Muscle	rectum
28	chr19:53495800-53497800	Active TSS	Aorta	Aorta
29	chr19:53496000-53496600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
30	chr19:53496000-53496600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
31	chr19:53496000-53496600	Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr19:53496000-53496600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr19:53496000-53496600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr19:53496000-53496800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
35	chr19:53496000-53496800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
36	chr19:53496000-53497000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr19:53496000-53497000	Enhancers	Fetal Brain Male	brain
38	chr19:53496000-53497000	Active TSS	NHEK	skin
39	chr19:53496000-53497200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
40	chr19:53496000-53497200	Active TSS	Esophagus	oesophagus
41	chr19:53496000-53497600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr19:53496000-53497600	Active TSS	Colon Smooth Muscle	Colon
43	chr19:53496000-53497600	Active TSS	Fetal Intestine Large	intestine
44	chr19:53496000-53497600	Active TSS	Fetal Intestine Small	intestine
45	chr19:53496000-53497600	Active TSS	Ovary	ovary
46	chr19:53496000-53497600	Active TSS	Right Atrium	heart
47	chr19:53496000-53497600	Active TSS	HSMM	muscle
48	chr19:53496000-53497600	Active TSS	K562	blood
49	chr19:53496000-53497600	Active TSS	NH-A	brain
50	chr19:53496000-53497600	Active TSS	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links