Variant report

Variant	rs58082927
Chromosome Location	chr6:54583073-54583074
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:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:54574954..54578587-chr6:54580352..54583856,5	MCF-7	breast:
2	chr6:54578251..54580318-chr6:54581650..54584206,2	MCF-7	breast:
3	chr6:54568299..54570747-chr6:54582453..54584898,3	MCF-7	breast:
4	chr6:54581649..54583716-chr6:54731091..54732634,2	MCF-7	breast:
5	chr6:54561293..54570100-chr6:54582505..54590247,14	MCF-7	breast:
6	chr6:54574192..54576279-chr6:54583056..54585185,2	MCF-7	breast:
7	chr6:54580831..54596896-chr6:54704751..54716103,89	MCF-7	breast:
8	chr6:54579097..54581073-chr6:54581334..54583325,2	MCF-7	breast:
9	chr6:54582146..54584053-chr6:54741073..54743084,2	MCF-7	breast:
10	chr6:54582065..54584949-chr6:54722187..54724387,3	MCF-7	breast:
11	chr6:54577593..54590845-chr6:54708062..54715554,67	MCF-7	breast:
12	chr6:54581970..54584648-chr6:54584800..54586441,2	MCF-7	breast:
13	chr6:54582003..54585202-chr6:54737626..54739872,3	MCF-7	breast:
14	chr6:54582713..54585752-chr6:54741876..54745709,4	MCF-7	breast:
15	chr6:54582865..54585119-chr6:54718425..54721186,2	MCF-7	breast:
16	chr6:54582733..54583294-chr6:54934014..54934701,2	MCF-7	breast:
17	chr6:54559803..54567776-chr6:54579525..54585377,11	MCF-7	breast:
18	chr6:54582596..54584566-chr6:55092481..55094780,2	MCF-7	breast:
19	chr6:54581587..54585941-chr6:54586924..54591451,7	MCF-7	breast:
20	chr6:54570566..54573467-chr6:54582462..54585489,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction
ENSG00000224984	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11962935	1.00[EUR][1000 genomes]
rs56798185	1.00[EUR][1000 genomes]
rs57567824	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58880219	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59257883	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913275	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9349730	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9357817	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9357818	1.00[EUR][1000 genomes]
rs9367588	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9367589	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9367590	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9367592	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9367596	1.00[AMR][1000 genomes]
rs9370329	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9370335	1.00[AMR][1000 genomes]
rs9382374	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9382377	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9382378	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9382379	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9382381	1.00[EUR][1000 genomes]
rs9382382	1.00[EUR][1000 genomes]
rs9382385	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9382386	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9382388	1.00[AMR][1000 genomes]
rs9382393	0.83[AMR][1000 genomes]
rs9382394	0.83[AMR][1000 genomes]
rs9382395	0.83[AMR][1000 genomes]
rs9395992	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9395993	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9395994	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9395998	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9396001	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54582200-54583200	Weak transcription	Fetal Stomach	stomach
2	chr6:54582400-54583800	Enhancers	NHEK	skin
3	chr6:54582400-54585000	Enhancers	Fetal Lung	lung
4	chr6:54582600-54583800	Enhancers	Stomach Mucosa	stomach
5	chr6:54582800-54584200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:54583000-54583200	Enhancers	Liver	Liver
7	chr6:54583000-54583200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr6:54583000-54583400	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr6:54583000-54583400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:54583000-54583400	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr6:54583000-54583400	Flanking Active TSS	Fetal Intestine Small	intestine
12	chr6:54583000-54583400	Weak transcription	Fetal Kidney	kidney
13	chr6:54583000-54583400	Active TSS	HMEC	breast
14	chr6:54583000-54583600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:54583000-54583800	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr6:54583000-54584000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:54583000-54584000	Enhancers	Fetal Intestine Large	intestine
18	chr6:54583000-54584000	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr6:54583000-54584200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:54583000-54584200	Active TSS	Duodenum Mucosa	Duodenum
21	chr6:54583000-54584600	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr6:54583000-54584600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:54583000-54584600	Enhancers	Fetal Brain Female	brain
24	chr6:54583000-54584800	Enhancers	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links