Variant report

Variant	rs28379688
Chromosome Location	chr5:90516747-90516748
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr5:90516747-90516840	GM20000	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:90516379..90518427-chr5:90685377..90687540,2	MCF-7	breast:
2	chr5:90457529..90462053-chr5:90513611..90518131,5	MCF-7	breast:
3	chr5:90513015..90523645-chr5:90674785..90682171,21	K562	blood:
4	chr5:90512455..90524285-chr5:90673793..90683360,52	MCF-7	breast:
5	chr5:90398592..90401389-chr5:90514877..90517516,2	MCF-7	breast:
6	chr5:90514693..90517546-chr5:90521705..90523239,2	MCF-7	breast:
7	chr5:90514828..90516837-chr5:90519482..90521543,2	MCF-7	breast:
8	chr5:90510244..90526030-chr5:90672528..90682389,53	MCF-7	breast:
9	chr5:90512732..90524610-chr5:90674652..90682171,24	K562	blood:
10	chr5:90514930..90517107-chr5:90575291..90577972,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000212930	TF binding region
ENSG00000113369	Chromatin interaction
ENSG00000234292	Chromatin interaction
ENSG00000251093	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10059932	0.97[EUR][1000 genomes]
rs10072875	0.89[EUR][1000 genomes]
rs10473941	0.97[EUR][1000 genomes]
rs10473942	0.97[EUR][1000 genomes]
rs10474344	0.89[EUR][1000 genomes]
rs10474345	0.89[EUR][1000 genomes]
rs13362365	0.94[EUR][1000 genomes]
rs28490868	0.97[EUR][1000 genomes]
rs2973471	0.80[EUR][1000 genomes]
rs4392660	0.80[EUR][1000 genomes]
rs55657470	0.97[EUR][1000 genomes]
rs55818598	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55989779	0.97[EUR][1000 genomes]
rs56082303	0.94[EUR][1000 genomes]
rs56320224	0.87[EUR][1000 genomes]
rs56410910	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57891485	0.97[EUR][1000 genomes]
rs58520625	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59967608	0.94[EUR][1000 genomes]
rs6877491	0.87[EUR][1000 genomes]
rs73773329	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73773330	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73773334	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73773337	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv508369	chr5:90487017-90518540	Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	4 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	chr5:90514200-90517200	Enhancers	Placenta Amnion	Placenta Amnion
2	chr5:90515200-90519200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:90515200-90519800	Enhancers	Placenta	Placenta
4	chr5:90515600-90517000	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr5:90515600-90519600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:90515600-90524200	Weak transcription	HMEC	breast
7	chr5:90515600-90524400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:90515800-90517800	Weak transcription	Stomach Mucosa	stomach
9	chr5:90515800-90519400	Weak transcription	NHDF-Ad	bronchial
10	chr5:90515800-90519600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:90515800-90520600	Weak transcription	HSMMtube	muscle
12	chr5:90516000-90519600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:90516000-90519600	Weak transcription	HSMM	muscle
14	chr5:90516200-90517800	Weak transcription	Colon Smooth Muscle	Colon
15	chr5:90516200-90519400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:90516200-90519400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr5:90516200-90519600	Weak transcription	Osteobl	bone
18	chr5:90516400-90517800	Weak transcription	A549	lung
19	chr5:90516400-90519400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:90516400-90520200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:90516600-90517000	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links