Variant report

Variant	rs12725140
Chromosome Location	chr1:57815685-57815686
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs12081029	0.89[EUR][1000 genomes]
rs12401342	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12404869	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12411278	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12734724	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12737167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12737593	0.95[AFR][1000 genomes]
rs12741031	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12743986	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12748450	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12756218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1557223	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17422457	1.00[ASN][1000 genomes]
rs17423736	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17423834	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17457585	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34088636	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34339837	0.95[AFR][1000 genomes]
rs34349049	0.95[AFR][1000 genomes]
rs34374446	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34458695	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34475805	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34553708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34591213	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34600157	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34707135	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34725826	0.95[AFR][1000 genomes]
rs35120429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35321467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35335448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35344722	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35349270	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35404211	0.95[AFR][1000 genomes]
rs35511416	0.95[AFR][1000 genomes]
rs3908772	0.95[AFR][1000 genomes]
rs56096668	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56156700	0.95[AFR][1000 genomes]
rs58075307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71642111	1.00[EUR][1000 genomes]
rs71642113	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71642115	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71642116	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71642117	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71642118	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs74074913	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs74074918	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs74074976	0.95[AFR][1000 genomes]
rs74074978	0.95[AFR][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	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv871943	chr1:57784144-57855876	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv871530	chr1:57793948-57858319	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv817216	chr1:57801783-58130775	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv871968	chr1:57803349-57858319	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57800000-57826600	Weak transcription	Left Ventricle	heart
2	chr1:57803200-57816000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:57808200-57822400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:57808800-57816600	Weak transcription	Right Ventricle	heart
5	chr1:57811600-57819200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:57811800-57816200	Weak transcription	Fetal Brain Male	brain
7	chr1:57812800-57817600	Enhancers	Fetal Heart	heart
8	chr1:57813600-57816200	Weak transcription	Brain Germinal Matrix	brain
9	chr1:57814600-57816000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:57814600-57819400	Weak transcription	Lung	lung
11	chr1:57814800-57815800	Weak transcription	Fetal Brain Female	brain
12	chr1:57814800-57816000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:57814800-57817600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:57815000-57816000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:57815000-57816000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:57815400-57816200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:57815400-57816600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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