Variant report

Variant	rs1012643
Chromosome Location	chr20:53278379-53278380
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1474763	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1997834	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2870337	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2870340	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2904389	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4362623	0.81[EUR][1000 genomes]
rs6014111	0.80[EUR][1000 genomes]
rs6014112	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6023474	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6023475	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6023477	0.81[AMR][1000 genomes]
rs6064102	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6068935	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6127251	0.97[AMR][1000 genomes];0.99[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	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	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
3	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
4	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
5	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53276000-53280600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr20:53276200-53278400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr20:53277000-53280600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr20:53277200-53278600	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr20:53277400-53279400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr20:53277600-53278400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
7	chr20:53277600-53279000	Enhancers	Fetal Brain Male	brain
8	chr20:53277600-53279200	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr20:53277600-53279600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
10	chr20:53277600-53279600	Enhancers	Brain Germinal Matrix	brain
11	chr20:53277800-53278400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
12	chr20:53277800-53279000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr20:53277800-53280200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
14	chr20:53278200-53278600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr20:53278200-53279600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr20:53278200-53280000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
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