Variant report

Variant	rs72803534
Chromosome Location	chr2:55783233-55783234
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55459554..55461240-chr2:55781259..55783403,2	MCF-7	breast:
2	chr2:55782828..55785578-chr2:55789792..55791305,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143947	Chromatin interaction
ENSG00000162994	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10496048	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17278009	0.81[AMR][1000 genomes]
rs17792577	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4643582	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60356354	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72801530	0.87[AMR][1000 genomes]
rs72801531	0.87[AMR][1000 genomes]
rs72801560	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72801562	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72801566	0.81[EUR][1000 genomes]
rs72801568	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72801571	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72801572	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72801575	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72801577	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72801580	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72801581	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72801584	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72801592	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72801594	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72801601	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72803508	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72803511	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72803513	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72803515	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72803520	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72803525	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72803527	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72803529	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72803530	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72803536	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72803541	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72803542	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72803543	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72803544	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72803546	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72803553	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72803566	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72803573	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72803576	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72803586	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72803588	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72803591	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72803595	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72805406	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72805414	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv874160	chr2:55713102-55828974	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats 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	11 gene(s)	inside rSNPs	diseases
5	nsv525434	chr2:55716650-55841640	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats 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 miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55747800-55784000	Weak transcription	Esophagus	oesophagus
2	chr2:55748000-55784000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:55748000-55788000	Weak transcription	Colonic Mucosa	Colon
4	chr2:55748000-55793800	Weak transcription	Psoas Muscle	Psoas
5	chr2:55752600-55788200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:55752600-55831400	Weak transcription	Stomach Mucosa	stomach
7	chr2:55753600-55786600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:55754000-55784000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:55758200-55783800	Weak transcription	Gastric	stomach
10	chr2:55758200-55784000	Weak transcription	Pancreas	Pancrea
11	chr2:55758600-55784000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr2:55760800-55788000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:55761000-55788200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:55762000-55783800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:55762200-55784000	Weak transcription	Right Ventricle	heart
16	chr2:55767000-55784000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:55769600-55816000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:55769800-55788200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:55770000-55787000	Strong transcription	Dnd41	blood
20	chr2:55770400-55818200	Weak transcription	Small Intestine	intestine
21	chr2:55770600-55821600	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr2:55770800-55815800	Strong transcription	Liver	Liver
23	chr2:55771200-55788000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:55771600-55788000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:55771800-55788200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr2:55772600-55788000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr2:55773000-55784000	Weak transcription	Aorta	Aorta
28	chr2:55773200-55783800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr2:55773200-55784200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:55773200-55786800	Weak transcription	Brain Substantia Nigra	brain
31	chr2:55774200-55783800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:55774400-55784000	Weak transcription	Lung	lung
33	chr2:55774800-55784000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:55774800-55784000	Weak transcription	Brain Angular Gyrus	brain
35	chr2:55775000-55783800	Weak transcription	Brain Hippocampus Middle	brain
36	chr2:55775200-55783800	Weak transcription	Spleen	Spleen
37	chr2:55775200-55798000	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr2:55775800-55788000	Strong transcription	Primary hematopoietic stem cells	blood
39	chr2:55776000-55789600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr2:55776600-55788400	Strong transcription	Primary B cells from cord blood	blood
41	chr2:55777600-55784000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr2:55778000-55784000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr2:55778200-55783800	Weak transcription	NHLF	lung
44	chr2:55778200-55784200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr2:55778600-55783800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr2:55778600-55784200	Weak transcription	K562	blood
47	chr2:55779400-55788200	Strong transcription	Primary B cells from peripheral blood	blood
48	chr2:55779400-55792200	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr2:55779400-55793000	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr2:55779400-55795000	Strong transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links