Variant report

Variant	rs4671258
Chromosome Location	chr2:55999893-55999894
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55994825..55997779-chr2:55998633..56001283,3	MCF-7	breast:
2	chr2:55998559..56000178-chr2:56148124..56150854,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115380	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11678312	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11679173	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11688992	0.90[CEU][hapmap];0.83[GIH][hapmap];0.86[EUR][1000 genomes]
rs11693381	0.86[EUR][1000 genomes]
rs1367229	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17369365	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163238	0.82[EUR][1000 genomes]
rs3748946	1.00[JPT][hapmap]
rs4671261	0.86[EUR][1000 genomes]
rs4672072	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55916998	0.82[EUR][1000 genomes]
rs55987978	0.81[EUR][1000 genomes]
rs56102096	0.82[EUR][1000 genomes]
rs57233927	0.82[EUR][1000 genomes]
rs59504093	0.82[EUR][1000 genomes]
rs60693760	0.82[EUR][1000 genomes]
rs6704679	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6705051	0.84[EUR][1000 genomes]
rs6735306	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs72797607	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72797613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72805666	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72805668	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72805673	0.86[EUR][1000 genomes]
rs72805674	0.86[EUR][1000 genomes]
rs72805675	0.86[EUR][1000 genomes]
rs72807714	0.82[EUR][1000 genomes]
rs72807727	0.82[EUR][1000 genomes]
rs72807728	0.82[EUR][1000 genomes]
rs72807744	0.82[EUR][1000 genomes]
rs72814246	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv999962	chr2:55976574-56011517	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv997683	chr2:55976574-56013875	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv431080	chr2:55988293-56011517	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55989400-56015000	Weak transcription	Aorta	Aorta
2	chr2:55997600-56000000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr2:55998200-56000200	Enhancers	HUVEC	blood vessel
4	chr2:55998400-56000000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr2:55999000-56000000	Enhancers	Hela-S3	cervix
6	chr2:55999200-56000000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:55999200-56000000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:55999200-56000000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:55999200-56000000	Enhancers	Fetal Intestine Small	intestine
10	chr2:55999200-56000000	Enhancers	HMEC	breast
11	chr2:55999200-56000000	Enhancers	HSMMtube	muscle
12	chr2:55999200-56000000	Enhancers	NHEK	skin
13	chr2:55999200-56000000	Enhancers	Osteobl	bone
14	chr2:55999400-56000000	Enhancers	Muscle Satellite Cultured Cells	--
15	chr2:55999400-56000000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:55999400-56000000	Enhancers	Brain Hippocampus Middle	brain
17	chr2:55999600-56000000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:55999600-56000000	Enhancers	Adipose Nuclei	Adipose
19	chr2:55999800-56000000	Enhancers	A549	lung
20	chr2:55999800-56003000	Weak transcription	Stomach Mucosa	stomach
21	chr2:55999800-56003400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links