Variant report

Variant	rs12809378
Chromosome Location	chr12:20860535-20860536
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12809210	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12811837	0.91[EUR][1000 genomes]
rs12819256	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12820620	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12831009	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1515779	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16915410	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16923129	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34000404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34167698	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34425791	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35018358	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35123559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67481714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71446707	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71446708	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71446709	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71446712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71446713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71446714	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71446715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7306841	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7960372	0.91[EUR][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	nsv1048067	chr12:20363755-20874845	Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv541408	chr12:20363755-20874845	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1043890	chr12:20659151-21309993	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv541410	chr12:20659151-21309993	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1054997	chr12:20682009-21292602	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv557704	chr12:20842041-20893980	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:20853200-20863200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr12:20860000-20881200	Weak transcription	Brain Hippocampus Middle	brain
3	chr12:20860200-20860600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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