Variant report

Variant	rs58488720
Chromosome Location	chr5:43233022-43233023
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:43230706..43233203-chr5:43482627..43484657,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151881	Chromatin interaction
ENSG00000249492	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10045186	0.88[EUR][1000 genomes]
rs10045460	0.94[EUR][1000 genomes]
rs10056788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10062177	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10066481	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10473304	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10473305	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10512819	0.88[EUR][1000 genomes]
rs13356344	0.88[EUR][1000 genomes]
rs16873170	0.88[EUR][1000 genomes]
rs28394528	0.88[EUR][1000 genomes]
rs28600138	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28697178	0.88[EUR][1000 genomes]
rs4421113	0.88[EUR][1000 genomes]
rs4428421	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55799546	0.88[EUR][1000 genomes]
rs6867229	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6868632	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6885598	0.88[EUR][1000 genomes]
rs6887169	0.94[EUR][1000 genomes]
rs72752582	0.94[EUR][1000 genomes]
rs72752598	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72752601	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73751045	0.88[EUR][1000 genomes]
rs73751047	0.88[EUR][1000 genomes]
rs7701546	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7709926	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9292866	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
7	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
8	nsv968170	chr5:43232089-43233193	Weak transcription Enhancers	Chromatin interactive region	2 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	chr5:43196200-43245400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:43209600-43245200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr5:43215600-43236800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr5:43226400-43233800	Weak transcription	GM12878-XiMat	blood
5	chr5:43231000-43245600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr5:43232000-43233200	Enhancers	Pancreas	Pancrea
7	chr5:43232200-43233200	Enhancers	Brain Substantia Nigra	brain
8	chr5:43232200-43233400	Enhancers	Gastric	stomach
9	chr5:43232200-43234000	Weak transcription	Brain Angular Gyrus	brain
10	chr5:43232200-43245400	Weak transcription	Brain Anterior Caudate	brain
11	chr5:43232400-43236600	Weak transcription	Adipose Nuclei	Adipose
12	chr5:43232800-43233400	Enhancers	Lung	lung
13	chr5:43232800-43246000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr5:43233000-43233800	Weak transcription	Liver	Liver
15	chr5:43233000-43238600	Weak transcription	K562	blood
16	chr5:43233000-43245200	Weak transcription	Brain Hippocampus Middle	brain

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