Variant report

Variant	rs966548
Chromosome Location	chr20:53298308-53298309
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:53284764..53285373-chr20:53297635..53298458,2	MCF-7	breast:
2	chr20:53298053..53298982-chr3:64703908..64704505,2	MCF-7	breast:
3	chr20:53296558..53298632-chr3:64515452..64516902,29	MCF-7	breast:
4	chr20:53294274..53296254-chr20:53296968..53298496,2	MCF-7	breast:
5	chr20:53296906..53298947-chr20:53330986..53333656,2	MCF-7	breast:
6	chr20:53264760..53267099-chr20:53297639..53299981,2	MCF-7	breast:
7	chr20:53297756..53299793-chr20:53421394..53423179,2	MCF-7	breast:
8	chr20:53298027..53298984-chr20:54756236..54756891,2	MCF-7	breast:
9	chr20:53297044..53298391-chr20:53342876..53343999,9	MCF-7	breast:
10	chr20:53296415..53300428-chr3:64512136..64516086,4	MCF-7	breast:
11	chr20:53297141..53300024-chr20:53303959..53305467,2	MCF-7	breast:
12	chr20:53297063..53298490-chr3:64703588..64704964,7	MCF-7	breast:
13	chr20:53297030..53299399-chr3:64518913..64520051,28	MCF-7	breast:
14	chr20:53296950..53299252-chr3:64517666..64520403,2	MCF-7	breast:
15	chr20:53296916..53298758-chr3:64518136..64520683,88	MCF-7	breast:
16	chr20:53293305..53299094-chr20:53306694..53312269,5	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1013660	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2870347	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6014127	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6014128	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6014130	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023481	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6023500	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6091947	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6098158	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6123404	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs993806	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs993807	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]

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	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	nsv586283	chr20:53288595-53311415	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53296800-53299600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr20:53297000-53298600	Enhancers	Duodenum Smooth Muscle	Duodenum
3	chr20:53297000-53299200	Enhancers	Brain Germinal Matrix	brain
4	chr20:53297200-53298600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr20:53297200-53298600	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr20:53297200-53298800	Enhancers	Fetal Brain Female	brain
7	chr20:53297200-53299000	Enhancers	Stomach Smooth Muscle	stomach
8	chr20:53297200-53299600	Enhancers	Fetal Stomach	stomach
9	chr20:53297600-53298400	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr20:53297600-53298600	Enhancers	Adipose Nuclei	Adipose
11	chr20:53297600-53298800	Enhancers	Fetal Lung	lung
12	chr20:53297600-53299000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr20:53297600-53299200	Enhancers	Fetal Brain Male	brain
14	chr20:53297800-53298600	Enhancers	Fetal Muscle Leg	muscle
15	chr20:53298000-53299000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr20:53298000-53299400	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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