Variant report

Variant	rs4953458
Chromosome Location	chr2:47305980-47305981
allele	C/T
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	chr2:47305124..47307804-chr2:47314133..47316358,4	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	chr2:47304999..47307834-chr2:47310076..47312199,2	MCF-7	breast:
5	chr2:47299662..47307017-chr2:47401146..47405423,11	MCF-7	breast:
6	chr2:47304449..47306633-chr2:47306977..47308538,2	MCF-7	breast:
7	chr2:47298364..47306534-chr2:47399903..47404660,8	K562	blood:
8	chr2:47304605..47306931-chr2:47316870..47318800,2	MCF-7	breast:
9	chr2:47297108..47300673-chr2:47304396..47307131,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1046263	1.00[JPT][hapmap]
rs1046267	1.00[JPT][hapmap]
rs1573958	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4952864	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4953457	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4953459	1.00[ASN][1000 genomes]
rs6544954	1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs7569495	1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9973596	1.00[JPT][hapmap];0.83[AMR][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:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47299200-47306000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:47300600-47310400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr2:47301000-47306600	Weak transcription	Brain Germinal Matrix	brain
4	chr2:47301600-47307200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr2:47302000-47306000	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr2:47302000-47306200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:47302000-47307200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr2:47302000-47307400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr2:47302200-47307400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:47302200-47308400	Enhancers	Lung	lung
11	chr2:47302400-47306800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:47302400-47307600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:47302400-47307600	Enhancers	Muscle Satellite Cultured Cells	--
14	chr2:47302400-47308400	Enhancers	Placenta	Placenta
15	chr2:47302600-47307400	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr2:47302600-47307600	Enhancers	NHDF-Ad	bronchial
17	chr2:47302600-47308400	Enhancers	Stomach Mucosa	stomach
18	chr2:47302800-47306000	Enhancers	Duodenum Mucosa	Duodenum
19	chr2:47302800-47306000	Genic enhancers	Fetal Intestine Small	intestine
20	chr2:47302800-47306400	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr2:47302800-47307000	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr2:47302800-47308200	Enhancers	Colonic Mucosa	Colon
23	chr2:47303200-47306000	Weak transcription	Fetal Thymus	thymus
24	chr2:47303200-47306800	Weak transcription	Fetal Brain Male	brain
25	chr2:47303200-47307000	Weak transcription	Fetal Brain Female	brain
26	chr2:47303200-47308400	Enhancers	Pancreas	Pancrea
27	chr2:47303400-47308800	Enhancers	Adipose Nuclei	Adipose
28	chr2:47303600-47306800	Weak transcription	Fetal Stomach	stomach
29	chr2:47303600-47307600	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr2:47303800-47308400	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr2:47304000-47306000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:47304200-47306000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:47304200-47306000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:47304200-47306000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr2:47304200-47306800	Weak transcription	Primary B cells from peripheral blood	blood
36	chr2:47304200-47310800	Weak transcription	Primary B cells from cord blood	blood
37	chr2:47304400-47306000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:47304400-47306000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:47304400-47306000	Weak transcription	Colon Smooth Muscle	Colon
40	chr2:47304400-47306200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:47304400-47306400	Weak transcription	Ovary	ovary
42	chr2:47304400-47307600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:47304600-47306000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr2:47304600-47306000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:47304600-47306000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:47304600-47306000	Weak transcription	Fetal Lung	lung
47	chr2:47304600-47306000	Weak transcription	Fetal Muscle Leg	muscle
48	chr2:47304600-47306000	Weak transcription	Right Ventricle	heart
49	chr2:47304600-47306200	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr2:47304600-47306200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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