Variant report

Variant	rs16999283
Chromosome Location	chr20:52882025-52882026
allele	G/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

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:52881988..52885819-chr20:52932723..52935221,3	MCF-7	breast:
2	chr20:52879121..52882080-chr20:53057033..53059146,2	MCF-7	breast:
3	chr20:52209254..52210865-chr20:52881648..52883949,2	MCF-7	breast:
4	chr20:52880252..52882480-chr9:34646132..34648657,2	MCF-7	breast:
5	chr20:52881900..52884717-chr20:52925408..52927187,2	MCF-7	breast:
6	chr20:52835744..52843522-chr20:52881395..52889377,15	MCF-7	breast:
7	chr20:52823141..52827110-chr20:52881540..52888271,10	MCF-7	breast:
8	chr20:52881899..52886453-chr20:53260602..53265051,8	MCF-7	breast:
9	chr20:52845835..52847665-chr20:52881455..52883980,2	MCF-7	breast:

No data

No data

No data

Variant related genes	Relation type
ENSG00000171940	Chromatin interaction
ENSG00000213930	Chromatin interaction
ENSG00000101132	Chromatin interaction
ENSG00000258728	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10485794	1.00[CEU][hapmap]
rs16999265	1.00[EUR][1000 genomes]
rs16999288	1.00[CEU][hapmap];0.84[YRI][hapmap];1.00[EUR][1000 genomes]
rs16999291	1.00[CEU][hapmap];0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs57095301	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58027221	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58144675	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59946156	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6127146	1.00[CEU][hapmap]
rs7262882	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7263226	1.00[EUR][1000 genomes]
rs7264698	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7270801	1.00[EUR][1000 genomes]
rs73914338	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73914339	1.00[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	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv834010	chr20:52759824-52932939	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv834011	chr20:52858341-53086042	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52872800-52883800	Weak transcription	Pancreas	Pancrea
2	chr20:52874200-52883600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr20:52874200-52884000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr20:52879800-52883800	Weak transcription	Osteobl	bone
5	chr20:52880400-52883400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr20:52880600-52884000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr20:52880800-52883400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr20:52880800-52883400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr20:52880800-52883600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr20:52881000-52884000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr20:52881200-52884000	Weak transcription	Fetal Lung	lung
12	chr20:52881200-52885000	Weak transcription	Fetal Stomach	stomach
13	chr20:52881400-52883400	Weak transcription	Ovary	ovary

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links