Variant report

Variant	rs16999288
Chromosome Location	chr20:52887031-52887032
allele	C/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:52884699..52888516-chr20:52964644..52967204,3	MCF-7	breast:
2	chr17:57919124..57923290-chr20:52886956..52890114,3	MCF-7	breast:
3	chr20:52823148..52829420-chr20:52882441..52888238,13	MCF-7	breast:
4	chr20:52884175..52887299-chr20:52959985..52962637,4	MCF-7	breast:
5	chr20:52885191..52887868-chr20:55839667..55841629,2	MCF-7	breast:
6	chr20:52883714..52887393-chr20:53262850..53265125,5	MCF-7	breast:
7	chr20:52885163..52887679-chr20:53176549..53178400,2	MCF-7	breast:
8	chr20:52835744..52843522-chr20:52881395..52889377,15	MCF-7	breast:
9	chr20:52823141..52827110-chr20:52881540..52888271,10	MCF-7	breast:
10	chr20:52886227..52888754-chr20:52977596..52979522,2	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10485794	1.00[CEU][hapmap]
rs16999265	1.00[EUR][1000 genomes]
rs16999283	1.00[CEU][hapmap];0.84[YRI][hapmap];1.00[EUR][1000 genomes]
rs16999291	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs57095301	1.00[EUR][1000 genomes]
rs58027221	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58144675	1.00[EUR][1000 genomes]
rs59946156	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6127146	1.00[CEU][hapmap]
rs7262882	0.81[AFR][1000 genomes]
rs7263226	1.00[EUR][1000 genomes]
rs7264698	1.00[EUR][1000 genomes]
rs7270801	1.00[EUR][1000 genomes]
rs73914338	1.00[EUR][1000 genomes]
rs73914339	1.00[EUR][1000 genomes]
rs8125542	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv962638	chr20:52883415-52917517	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv178887	chr20:52885413-52894836	Enhancers Weak transcription	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52884000-52889400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr20:52884600-52889200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr20:52885000-52889600	Weak transcription	Pancreas	Pancrea
4	chr20:52885200-52889600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr20:52885200-52889600	Weak transcription	Ovary	ovary
6	chr20:52885600-52889000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr20:52885800-52889200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr20:52885800-52889600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr20:52886000-52889200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr20:52886000-52889200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr20:52886200-52889200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr20:52886200-52889200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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

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