Variant report

Variant	rs6544954
Chromosome Location	chr2:47303631-47303632
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47212859..47216615-chr2:47301507..47304672,4	MCF-7	breast:
2	chr2:47303169..47307562-chr2:47312603..47317235,6	MCF-7	breast:
3	chr2:47295023..47298657-chr2:47300855..47310213,9	MCF-7	breast:
4	chr2:47299662..47307017-chr2:47401146..47405423,11	MCF-7	breast:
5	chr2:47302688..47305561-chr2:47417562..47420065,2	MCF-7	breast:
6	chr2:47303567..47305650-chr2:47402642..47405179,3	MCF-7	breast:
7	chr2:47301037..47304852-chr2:47397378..47400468,3	MCF-7	breast:
8	chr2:47302270..47304198-chr2:47307298..47308850,2	MCF-7	breast:
9	chr2:47298364..47306534-chr2:47399903..47404660,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1046263	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1046267	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1573958	0.94[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2570511	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4952864	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4953457	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4953458	1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs7569495	1.00[JPT][hapmap];0.88[AMR][1000 genomes]
rs940737	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9973596	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS 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 miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv984437	chr2:47270533-47307361	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv873998	chr2:47273732-47313624	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47298000-47304400	Genic enhancers	Spleen	Spleen
2	chr2:47298800-47305200	Strong transcription	Thymus	Thymus
3	chr2:47299200-47304800	Strong transcription	Primary T cells from cord blood	blood
4	chr2:47299200-47306000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:47299400-47303800	Genic enhancers	Stomach Smooth Muscle	stomach
6	chr2:47300400-47303800	Genic enhancers	Primary monocytes fromperipheralblood	blood
7	chr2:47300600-47304000	Weak transcription	Ovary	ovary
8	chr2:47300600-47310400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:47300800-47304000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:47301000-47303800	Weak transcription	Small Intestine	intestine
11	chr2:47301000-47304600	Enhancers	HSMM	muscle
12	chr2:47301000-47306600	Weak transcription	Brain Germinal Matrix	brain
13	chr2:47301200-47304800	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr2:47301200-47305200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:47301200-47305800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr2:47301400-47303800	Weak transcription	Esophagus	oesophagus
17	chr2:47301600-47307200	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr2:47301800-47304200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr2:47301800-47304600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:47302000-47303800	Genic enhancers	NHLF	lung
21	chr2:47302000-47304200	Strong transcription	Primary B cells from peripheral blood	blood
22	chr2:47302000-47305400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:47302000-47306000	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr2:47302000-47306200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:47302000-47307200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:47302000-47307400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr2:47302200-47304200	Strong transcription	Primary B cells from cord blood	blood
28	chr2:47302200-47304400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr2:47302200-47304600	Enhancers	Fetal Muscle Trunk	muscle
30	chr2:47302200-47305400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:47302200-47307400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:47302200-47308400	Enhancers	Lung	lung
33	chr2:47302400-47304200	Enhancers	Brain Substantia Nigra	brain
34	chr2:47302400-47304800	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr2:47302400-47305200	Enhancers	HUVEC	blood vessel
36	chr2:47302400-47305400	Enhancers	NH-A	brain
37	chr2:47302400-47306800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:47302400-47307600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:47302400-47307600	Enhancers	Muscle Satellite Cultured Cells	--
40	chr2:47302400-47308400	Enhancers	Placenta	Placenta
41	chr2:47302600-47304000	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr2:47302600-47304200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:47302600-47304400	Enhancers	Brain Cingulate Gyrus	brain
44	chr2:47302600-47304400	Enhancers	Colon Smooth Muscle	Colon
45	chr2:47302600-47304600	Enhancers	Fetal Lung	lung
46	chr2:47302600-47304600	Enhancers	Left Ventricle	heart
47	chr2:47302600-47304600	Enhancers	Right Ventricle	heart
48	chr2:47302600-47304800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr2:47302600-47304800	Enhancers	H1 Cell Line	embryonic stem cell
50	chr2:47302600-47304800	Enhancers	Fetal Heart	heart

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