Variant report

Variant	rs2561529
Chromosome Location	chr19:41226109-41226110
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41220314-41228780	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr19:41220376-41228744	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:24 , 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	chr19:41224337..41226397-chr19:41306033..41307626,2	K562	blood:
9	chr19:41224377..41227042-chr19:41281377..41283783,3	MCF-7	breast:
10	chr19:41224564..41226766-chr3:161088576..161090786,2	MCF-7	breast:
11	chr19:41224657..41226437-chr19:41266206..41269077,2	MCF-7	breast:
12	chr19:41225224..41227952-chr19:41245122..41248446,3	MCF-7	breast:
13	chr19:41219701..41226727-chr19:41253156..41258804,17	K562	blood:
14	chr19:41224979..41226592-chr19:41227722..41229766,2	K562	blood:
15	chr19:41224721..41227148-chr19:41302837..41304471,2	K562	blood:
16	chr19:41191453..41200740-chr19:41219595..41226457,20	MCF-7	breast:
17	chr19:41224929..41227139-chr19:41232897..41235326,2	K562	blood:
18	chr19:41223813..41226637-chr19:41310296..41313871,3	MCF-7	breast:
19	chr19:41219625..41226874-chr19:41252287..41258959,29	MCF-7	breast:
20	chr19:41116192..41118277-chr19:41225269..41226829,2	MCF-7	breast:
21	chr19:41225019..41226612-chr19:41226846..41228411,3	MCF-7	breast:
22	chr19:41219350..41226574-chr19:41253922..41258567,22	MCF-7	breast:
23	chr19:41223981..41226562-chr19:41304181..41307698,5	MCF-7	breast:
24	chr19:41224545..41226553-chr19:41238187..41240048,2	MCF-7	breast:

No data

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

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10420651	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10420685	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1455434	0.81[EUR][1000 genomes]
rs1531063	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1869710	0.81[EUR][1000 genomes]
rs2254326	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2254338	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2303723	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2561531	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2607418	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34633896	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3745212	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7250888	0.84[EUR][1000 genomes]

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

No data

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	chr19:41220600-41226400	Active TSS	Right Atrium	heart
3	chr19:41220600-41227000	Active TSS	Esophagus	oesophagus
4	chr19:41220800-41226200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr19:41221400-41226200	Active TSS	HMEC	breast
6	chr19:41221600-41226400	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr19:41222400-41226800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr19:41222400-41227000	Active TSS	Lung	lung
9	chr19:41222600-41226200	Active TSS	HSMMtube	muscle
10	chr19:41223400-41226800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr19:41223400-41227200	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr19:41223400-41227200	Flanking Active TSS	HUVEC	blood vessel
13	chr19:41223400-41227400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr19:41223600-41226200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr19:41223600-41226400	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr19:41223800-41226400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr19:41224000-41227200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr19:41224400-41226600	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr19:41224400-41227200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr19:41224400-41227200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr19:41224600-41227200	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr19:41224800-41226400	Flanking Active TSS	Placenta	Placenta
23	chr19:41224800-41227000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr19:41224800-41228600	Enhancers	Fetal Brain Male	brain
25	chr19:41225000-41227200	Enhancers	Fetal Heart	heart
26	chr19:41225000-41228400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr19:41225200-41226200	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr19:41225200-41226200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr19:41225200-41226400	Enhancers	Primary B cells from peripheral blood	blood
30	chr19:41225200-41226400	Enhancers	Primary T cells fromperipheralblood	blood
31	chr19:41225200-41226400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr19:41225200-41226400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr19:41225200-41226400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr19:41225200-41226400	Active TSS	Brain Angular Gyrus	brain
35	chr19:41225200-41227200	Enhancers	Ovary	ovary
36	chr19:41225200-41227200	Enhancers	Spleen	Spleen
37	chr19:41225200-41227400	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr19:41225200-41228000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr19:41225200-41229200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr19:41225200-41229400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr19:41225200-41235200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr19:41225200-41238800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:41225200-41243200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr19:41225400-41226800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr19:41225400-41227000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr19:41225400-41227200	Flanking Active TSS	Brain Hippocampus Middle	brain
47	chr19:41225400-41227200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
48	chr19:41225400-41231000	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr19:41225600-41226400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr19:41225600-41226400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links