Variant report

Variant	rs392646
Chromosome Location	chr20:53555547-53555548
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:62392588..62393414-chr20:53555074..53555763,2	MCF-7	breast:
2	chr17:62386547..62391340-chr20:53548880..53558881,15	MCF-7	breast:
3	chr20:45825058..45825592-chr20:53555003..53555747,2	MCF-7	breast:
4	chr17:62397851..62398803-chr20:53555134..53556107,4	MCF-7	breast:
5	chr20:53555216..53557434-chr3:64517545..64519675,2	MCF-7	breast:
6	chr20:53555329..53555881-chr3:64519295..64520243,2	MCF-7	breast:
7	chr20:53553719..53556075-chr20:53557124..53559804,2	MCF-7	breast:
8	chr20:53554839..53555823-chr3:64515857..64516498,2	MCF-7	breast:
9	chr2:118571843..118572636-chr20:53555097..53555794,2	MCF-7	breast:
10	chr17:62388537..62389481-chr20:53555289..53556141,2	MCF-7	breast:
11	chr17:62386971..62389896-chr20:53555496..53558705,8	MCF-7	breast:
12	chr20:53554975..53555769-chr3:64657740..64658419,2	MCF-7	breast:
13	chr20:53554525..53556121-chr3:64518981..64520313,12	MCF-7	breast:
14	chr20:53555243..53556146-chr3:64469688..64470320,3	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:15)

rs_ID	r²[population]
rs1125961	0.86[ASN][1000 genomes]
rs1499870	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs159080	0.81[EUR][1000 genomes]
rs17267366	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2022186	0.86[ASN][1000 genomes]
rs288829	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs373968	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs415667	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs423867	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs430767	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs451817	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6123433	0.86[ASN][1000 genomes]
rs6127331	0.86[ASN][1000 genomes]
rs6127333	0.86[ASN][1000 genomes]
rs6127334	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067497	chr20:53146241-53751820	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
2	nsv1064144	chr20:53175264-53750137	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv544302	chr20:53175264-53750137	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	nsv1060552	chr20:53234716-53655115	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv521883	chr20:53497139-53563837	Enhancers Active TSS Flanking Active TSS Weak transcription	Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv524442	chr20:53497139-53563837	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53555200-53556200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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