Variant report

Variant	rs490015
Chromosome Location	chr19:56600527-56600528
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:56600333..56603154-chr19:56649687..56651196,2	K562	blood:
2	chr17:41464187..41466335-chr19:56598175..56601155,2	K562	blood:
3	chr17:41464708..41466373-chr19:56599655..56601155,2	MCF-7	breast:
4	chr19:56599644..56602994-chr19:56620278..56624249,5	K562	blood:
5	chr19:56600362..56602994-chr19:56622256..56625120,2	K562	blood:

Variant related genes	Relation type
ENSG00000188825	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs473045	0.88[ASN][1000 genomes]
rs496526	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs499083	0.88[ASN][1000 genomes]
rs511610	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511642	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs529291	0.88[ASN][1000 genomes]
rs546082	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs562907	0.88[ASN][1000 genomes]
rs587252	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs629836	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056598	chr19:56331762-56703428	Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
2	nsv1062406	chr19:56382492-56602374	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1058988	chr19:56382492-56609032	Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1064371	chr19:56418215-56842450	ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
5	nsv1057316	chr19:56418215-56849458	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
6	nsv580354	chr19:56505685-56723492	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
7	nsv833883	chr19:56512601-56640089	Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
8	nsv523651	chr19:56537528-56707048	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
9	nsv1057820	chr19:56555942-56720262	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
10	nsv528998	chr19:56578238-56707048	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
11	nsv912512	chr19:56592286-56636759	Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
12	nsv517365	chr19:56592286-56674548	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
13	nsv912513	chr19:56592286-56685463	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
14	nsv521744	chr19:56592286-56686953	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
15	nsv912514	chr19:56596815-56636759	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
16	esv3338193	chr19:56598165-56601513	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
17	esv3409501	chr19:56598390-56601188	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
18	nsv912515	chr19:56598829-56623710	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56592600-56620000	Weak transcription	HSMMtube	muscle
2	chr19:56592800-56601200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr19:56592800-56602200	Weak transcription	NH-A	brain
4	chr19:56592800-56602400	Weak transcription	Brain Anterior Caudate	brain
5	chr19:56592800-56602800	Weak transcription	Right Atrium	heart
6	chr19:56592800-56622600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr19:56593000-56600600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr19:56593000-56601000	Weak transcription	Brain Hippocampus Middle	brain
9	chr19:56593000-56601600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr19:56593000-56602200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr19:56593000-56602200	Weak transcription	Brain Substantia Nigra	brain
12	chr19:56593000-56602400	Weak transcription	Osteobl	bone
13	chr19:56593000-56606400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr19:56593000-56616200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr19:56593000-56616600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr19:56593000-56616800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr19:56593000-56631200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr19:56593200-56600800	Weak transcription	Primary B cells from cord blood	blood
19	chr19:56593200-56600800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr19:56593600-56616000	Weak transcription	Stomach Mucosa	stomach
21	chr19:56594800-56616800	Weak transcription	HUVEC	blood vessel
22	chr19:56595200-56601000	Weak transcription	K562	blood
23	chr19:56595400-56600600	Weak transcription	NHEK	skin
24	chr19:56595400-56601200	Weak transcription	HSMM	muscle
25	chr19:56596000-56601800	Genic enhancers	Spleen	Spleen
26	chr19:56596200-56603400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr19:56596400-56605400	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr19:56596600-56600800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr19:56596600-56601000	Strong transcription	Pancreas	Pancrea
30	chr19:56596600-56601800	Strong transcription	Lung	lung
31	chr19:56596600-56601800	Strong transcription	NHLF	lung
32	chr19:56596600-56602800	Strong transcription	Fetal Stomach	stomach
33	chr19:56596600-56603600	Strong transcription	Fetal Intestine Small	intestine
34	chr19:56596600-56604000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr19:56596600-56604200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr19:56596600-56604400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr19:56596600-56604600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr19:56596600-56614800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr19:56596800-56602200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:56596800-56603000	Strong transcription	Duodenum Mucosa	Duodenum
41	chr19:56597000-56601000	Weak transcription	Fetal Lung	lung
42	chr19:56597000-56602600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr19:56597000-56603600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr19:56597000-56604000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr19:56597200-56600600	Weak transcription	Rectal Smooth Muscle	rectum
46	chr19:56597200-56602400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr19:56597200-56619400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr19:56597400-56600600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr19:56597400-56601400	Weak transcription	HMEC	breast
50	chr19:56597400-56602200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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