Variant report

Variant	rs58394027
Chromosome Location	chr2:48333882-48333883
allele	A/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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:48132095..48134288-chr2:48331229..48334150,2	MCF-7	breast:
2	chr2:48133526..48134627-chr2:48333164..48334071,4	MCF-7	breast:
3	chr2:48332416..48334392-chr2:48540210..48543027,2	MCF-7	breast:
4	chr2:48085009..48085603-chr2:48333401..48334249,2	MCF-7	breast:
5	chr2:48084628..48085620-chr2:48332904..48334295,6	MCF-7	breast:
6	chr2:48134122..48134992-chr2:48333400..48334251,2	K562	blood:
7	chr2:48084941..48085583-chr2:48333822..48334364,3	K562	blood:
8	chr2:48133747..48134281-chr2:48333708..48334343,2	MCF-7	breast:
9	chr2:48132762..48136318-chr2:48332374..48334594,3	K562	blood:
10	chr2:48333414..48334265-chr2:48647971..48648489,2	K562	blood:
11	chr2:48304303..48309230-chr2:48331532..48334851,4	K562	blood:
12	chr2:48117409..48117947-chr2:48333790..48334356,2	K562	blood:
13	chr2:48331367..48333886-chr2:48667621..48669155,2	MCF-7	breast:
14	chr2:48333421..48335488-chr2:48695315..48698262,2	K562	blood:
15	chr2:48084089..48084724-chr2:48333394..48334291,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000162869	Chromatin interaction
ENSG00000170802	Chromatin interaction
ENSG00000138081	Chromatin interaction
ENSG00000272663	Chromatin interaction
ENSG00000233230	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11893417	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11897391	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11898242	1.00[AMR][1000 genomes]
rs11899162	1.00[AMR][1000 genomes]
rs11901147	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1396827	1.00[AMR][1000 genomes]
rs1483211	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1483212	1.00[AMR][1000 genomes]
rs17037095	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17037118	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17037121	1.00[AMR][1000 genomes]
rs17037139	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17037152	1.00[AMR][1000 genomes]
rs17037198	1.00[AMR][1000 genomes]
rs28702589	1.00[AMR][1000 genomes]
rs2881937	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55876292	1.00[AMR][1000 genomes]
rs55877668	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56136838	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56162077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56244209	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57023060	1.00[AMR][1000 genomes]
rs57488672	1.00[AMR][1000 genomes]
rs60806982	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61615260	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73927905	0.82[AFR][1000 genomes]
rs73927914	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73927920	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73927925	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73927926	1.00[AMR][1000 genomes]
rs73927927	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73927928	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73927929	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73927931	1.00[AMR][1000 genomes]
rs73927934	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73927935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73927937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73927938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73927940	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73927942	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73927945	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73927946	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73927949	1.00[AMR][1000 genomes]
rs73927950	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73927951	1.00[AMR][1000 genomes]
rs73927955	1.00[AMR][1000 genomes]
rs73927956	1.00[AMR][1000 genomes]
rs73927960	1.00[AMR][1000 genomes]
rs73927961	1.00[AMR][1000 genomes]
rs73927962	1.00[AMR][1000 genomes]
rs7568794	0.84[AFR][1000 genomes];1.00[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	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS 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	36 gene(s)	inside rSNPs	diseases
3	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1000455	chr2:48202161-48362638	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv581773	chr2:48277490-48443109	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48332800-48334000	Enhancers	NH-A	brain
2	chr2:48333000-48334000	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr2:48333000-48334000	Enhancers	H9 Cell Line	embryonic stem cell
4	chr2:48333000-48334000	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr2:48333000-48334000	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr2:48333000-48334000	Enhancers	HUVEC	blood vessel
7	chr2:48333000-48334400	Enhancers	Pancreas	Pancrea
8	chr2:48333000-48335000	Enhancers	H1 Cell Line	embryonic stem cell
9	chr2:48333000-48335000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:48333000-48335000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:48333000-48335000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr2:48333000-48335000	Enhancers	K562	blood
13	chr2:48333200-48334000	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr2:48333200-48334000	Active TSS	Brain Anterior Caudate	brain
15	chr2:48333200-48334000	Enhancers	Fetal Heart	heart
16	chr2:48333200-48334200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:48333200-48334200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:48333200-48334200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:48333200-48334400	Enhancers	Brain Germinal Matrix	brain
20	chr2:48333200-48334400	Enhancers	Fetal Stomach	stomach
21	chr2:48333200-48334400	Enhancers	Fetal Thymus	thymus
22	chr2:48333200-48334400	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr2:48333200-48334400	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr2:48333200-48334600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:48333200-48334600	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr2:48333200-48334800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr2:48333200-48335000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:48333200-48335000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:48333200-48335000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:48333200-48335000	Enhancers	Placenta	Placenta
31	chr2:48333200-48335000	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr2:48333200-48335000	Enhancers	Spleen	Spleen
33	chr2:48333200-48335200	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr2:48333200-48335200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:48333200-48335200	Enhancers	NHLF	lung
36	chr2:48333200-48338200	Enhancers	HMEC	breast
37	chr2:48333400-48334000	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr2:48333400-48334000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr2:48333400-48334000	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr2:48333400-48334000	Flanking Active TSS	Dnd41	blood
41	chr2:48333400-48334200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:48333400-48334200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:48333400-48334200	Enhancers	Primary B cells from cord blood	blood
44	chr2:48333400-48334200	Enhancers	Primary B cells from peripheral blood	blood
45	chr2:48333400-48334200	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr2:48333400-48334200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr2:48333400-48334200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:48333400-48334200	Active TSS	Brain Substantia Nigra	brain
49	chr2:48333400-48334200	Flanking Active TSS	Fetal Intestine Small	intestine
50	chr2:48333400-48334200	Active TSS	Pancreatic Islets	Pancreatic Islet

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