Variant report

Variant	rs10411461
Chromosome Location	chr19:53040468-53040469
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53039676..53041332-chr19:53072309..53073853,2	MCF-7	breast:
2	chr19:53039880..53042500-chr19:53052327..53054340,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167562	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11882836	1.00[EUR][1000 genomes]
rs2162932	1.00[EUR][1000 genomes]
rs2447422	1.00[EUR][1000 genomes]
rs2931759	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2931760	1.00[EUR][1000 genomes]
rs55753173	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57548816	1.00[EUR][1000 genomes]
rs58325433	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59230195	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60194947	1.00[EUR][1000 genomes]
rs60238878	1.00[EUR][1000 genomes]
rs60404252	1.00[EUR][1000 genomes]
rs60856351	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73576268	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73576294	1.00[EUR][1000 genomes]
rs73578242	1.00[EUR][1000 genomes]
rs73584860	1.00[EUR][1000 genomes]
rs73584871	1.00[EUR][1000 genomes]
rs73584874	1.00[EUR][1000 genomes]
rs73586713	1.00[EUR][1000 genomes]
rs73934550	1.00[EUR][1000 genomes]
rs73934555	1.00[EUR][1000 genomes]
rs8109739	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8110537	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv580026	chr19:52937100-53059872	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1063648	chr19:52938131-53041119	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv978841	chr19:52983057-53088237	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1066717	chr19:52993620-53041995	Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1064342	chr19:52996710-53041119	ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1055859	chr19:53001299-53041119	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1060656	chr19:53001299-53041995	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv510772	chr19:53037211-53103470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53032200-53057000	Weak transcription	Hela-S3	cervix
2	chr19:53032600-53049800	Weak transcription	HepG2	liver
3	chr19:53037600-53051800	Weak transcription	K562	blood
4	chr19:53038000-53040800	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr19:53038600-53040600	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr19:53038600-53040600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:53038600-53040800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr19:53039000-53052200	Weak transcription	Fetal Brain Male	brain
9	chr19:53039200-53056000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
10	chr19:53039600-53052000	Weak transcription	HSMMtube	muscle
11	chr19:53039800-53040600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
12	chr19:53039800-53040600	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr19:53039800-53040600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr19:53039800-53040600	Flanking Active TSS	Dnd41	blood
15	chr19:53039800-53046000	Weak transcription	Stomach Mucosa	stomach
16	chr19:53039800-53046200	Weak transcription	Aorta	Aorta
17	chr19:53039800-53050600	Weak transcription	Fetal Lung	lung
18	chr19:53039800-53051600	Weak transcription	Brain Substantia Nigra	brain
19	chr19:53039800-53051600	Weak transcription	Fetal Kidney	kidney
20	chr19:53040000-53040800	Enhancers	Primary B cells from peripheral blood	blood
21	chr19:53040000-53042400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr19:53040000-53043200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr19:53040000-53045000	Weak transcription	NH-A	brain
24	chr19:53040000-53046000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr19:53040000-53046200	Weak transcription	Brain Anterior Caudate	brain
26	chr19:53040000-53046200	Weak transcription	Left Ventricle	heart
27	chr19:53040000-53046600	Weak transcription	Gastric	stomach
28	chr19:53040000-53046600	Weak transcription	Ovary	ovary
29	chr19:53040000-53046800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr19:53040000-53046800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr19:53040000-53046800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr19:53040000-53046800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr19:53040000-53047400	Weak transcription	Brain Hippocampus Middle	brain
34	chr19:53040000-53047400	Weak transcription	HSMM	muscle
35	chr19:53040000-53047600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr19:53040000-53051600	Weak transcription	Brain Angular Gyrus	brain
37	chr19:53040000-53051800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr19:53040000-53052000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:53040000-53052200	Weak transcription	Psoas Muscle	Psoas
40	chr19:53040000-53054400	Weak transcription	Fetal Heart	heart
41	chr19:53040200-53040600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr19:53040200-53040600	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr19:53040200-53040800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
44	chr19:53040200-53041000	Enhancers	Primary T cells fromperipheralblood	blood
45	chr19:53040200-53041000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr19:53040200-53041000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr19:53040200-53041000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr19:53040200-53041400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr19:53040200-53041800	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr19:53040200-53041800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links