Variant report

Variant	rs2561528
Chromosome Location	chr19:41226415-41226416
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR3C1	chr19:41226333-41226838	A549	lung:	n/a	n/a
2	NR3C1	chr19:41226358-41226867	A549	lung:	n/a	n/a
3	POLR2A	chr19:41226334-41227050	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr19:41220314-41228780	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr19:41226267-41226867	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr19:41220376-41228744	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr19:41226175-41226944	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr19:41226399-41226788	HUVEC	blood vessel:	n/a	n/a
9	NR3C1	chr19:41226285-41227007	A549	lung:	n/a	n/a
10	STAT3	chr19:41226399-41226902	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr19:41226128-41226490	HepG2	liver:	n/a	n/a
12	NR3C1	chr19:41226352-41226955	A549	lung:	n/a	n/a

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41219786..41224599-chr19:41225550..41230033,6	K562	blood:
2	chr19:41224831..41226803-chr19:41249457..41251875,2	K562	blood:
3	chr19:41224824..41227088-chr19:41310622..41313092,2	MCF-7	breast:
4	chr19:41220369..41226479-chr19:41305318..41310706,7	K562	blood:
5	chr19:41225203..41228152-chr19:41229042..41232599,3	MCF-7	breast:
6	chr19:41225475..41227295-chr19:41243418..41244971,2	K562	blood:
7	chr19:41225541..41227070-chr19:41249613..41252351,2	MCF-7	breast:
8	chr19:41224377..41227042-chr19:41281377..41283783,3	MCF-7	breast:
9	chr19:41224564..41226766-chr3:161088576..161090786,2	MCF-7	breast:
10	chr19:41224657..41226437-chr19:41266206..41269077,2	MCF-7	breast:
11	chr19:41225224..41227952-chr19:41245122..41248446,3	MCF-7	breast:
12	chr19:41219701..41226727-chr19:41253156..41258804,17	K562	blood:
13	chr19:41224979..41226592-chr19:41227722..41229766,2	K562	blood:
14	chr19:41224721..41227148-chr19:41302837..41304471,2	K562	blood:
15	chr19:41191453..41200740-chr19:41219595..41226457,20	MCF-7	breast:
16	chr19:41224929..41227139-chr19:41232897..41235326,2	K562	blood:
17	chr19:41223813..41226637-chr19:41310296..41313871,3	MCF-7	breast:
18	chr19:41219625..41226874-chr19:41252287..41258959,29	MCF-7	breast:
19	chr19:41116192..41118277-chr19:41225269..41226829,2	MCF-7	breast:
20	chr19:41225019..41226612-chr19:41226846..41228411,3	MCF-7	breast:
21	chr19:41219350..41226574-chr19:41253922..41258567,22	MCF-7	breast:
22	chr19:41223981..41226562-chr19:41304181..41307698,5	MCF-7	breast:
23	chr19:41224545..41226553-chr19:41238187..41240048,2	MCF-7	breast:

No data

Variant related genes	Relation type
ADCK4	TF binding region
ENSG00000196542	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000090006	Chromatin interaction
ENSG00000269858	Chromatin interaction
ENSG00000268797	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000105245	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11538385	1.00[JPT][hapmap]
rs2561530	0.89[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2561536	0.82[JPT][hapmap]
rs2604888	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2604913	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2607420	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv1067017	chr19:41185992-41231251	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2561528	ZNF574	cis	parietal	SCAN
rs2561528	ADCK4	cis	multi-tissue	Pritchard
rs2561528	BCAT2	cis	cerebellum	SCAN
rs2561528	KCNN4	cis	cerebellum	SCAN
rs2561528	C19orf54	cis	lymphoblastoid	seeQTL
rs2561528	LIN7B	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41220400-41226800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr19:41220600-41227000	Active TSS	Esophagus	oesophagus
3	chr19:41222400-41226800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:41222400-41227000	Active TSS	Lung	lung
5	chr19:41223400-41226800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr19:41223400-41227200	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr19:41223400-41227200	Flanking Active TSS	HUVEC	blood vessel
8	chr19:41223400-41227400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr19:41224000-41227200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:41224400-41226600	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr19:41224400-41227200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr19:41224400-41227200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
13	chr19:41224600-41227200	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr19:41224800-41227000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr19:41224800-41228600	Enhancers	Fetal Brain Male	brain
16	chr19:41225000-41227200	Enhancers	Fetal Heart	heart
17	chr19:41225000-41228400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr19:41225200-41227200	Enhancers	Ovary	ovary
19	chr19:41225200-41227200	Enhancers	Spleen	Spleen
20	chr19:41225200-41227400	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr19:41225200-41228000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr19:41225200-41229200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr19:41225200-41229400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr19:41225200-41235200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr19:41225200-41238800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:41225200-41243200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr19:41225400-41226800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr19:41225400-41227000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr19:41225400-41227200	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr19:41225400-41227200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
31	chr19:41225400-41231000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr19:41225600-41226600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr19:41225600-41226600	Enhancers	Primary B cells from cord blood	blood
34	chr19:41225600-41226600	Enhancers	Fetal Lung	lung
35	chr19:41225600-41226600	Flanking Active TSS	HepG2	liver
36	chr19:41225600-41226600	Flanking Active TSS	NHEK	skin
37	chr19:41225600-41226800	Enhancers	Primary T cells from cord blood	blood
38	chr19:41225600-41226800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr19:41225600-41226800	Weak transcription	Small Intestine	intestine
40	chr19:41225600-41227200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr19:41225600-41227200	Enhancers	Fetal Thymus	thymus
42	chr19:41225600-41229800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr19:41225600-41231600	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr19:41225800-41226800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr19:41225800-41226800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr19:41225800-41226800	Enhancers	NH-A	brain
47	chr19:41225800-41227000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr19:41225800-41227000	Active TSS	Right Ventricle	heart
49	chr19:41225800-41227200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr19:41225800-41228000	Weak transcription	A549	lung

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