Variant report

Variant	rs172397
Chromosome Location	chr5:58034515-58034516
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1035393	0.95[EUR][1000 genomes]
rs1422226	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs149351	0.85[EUR][1000 genomes]
rs149525	0.89[EUR][1000 genomes]
rs158987	0.87[EUR][1000 genomes]
rs158999	0.81[EUR][1000 genomes]
rs159000	0.81[EUR][1000 genomes]
rs159003	0.81[EUR][1000 genomes]
rs159004	0.82[EUR][1000 genomes]
rs159006	0.82[EUR][1000 genomes]
rs159007	0.82[EUR][1000 genomes]
rs172398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs176637	0.87[EUR][1000 genomes]
rs176807	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs182391	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs186010	0.86[EUR][1000 genomes]
rs1895232	0.97[EUR][1000 genomes]
rs2545789	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2591920	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2591922	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs290572	0.86[EUR][1000 genomes]
rs292948	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs292949	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293000	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293002	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293005	0.98[EUR][1000 genomes]
rs293006	0.94[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs293007	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs293008	0.94[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs293009	0.91[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs293010	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293013	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs293014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293018	0.93[EUR][1000 genomes]
rs293019	0.95[EUR][1000 genomes]
rs293025	0.95[EUR][1000 genomes]
rs293026	0.97[EUR][1000 genomes]
rs293027	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs293029	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs368762	0.80[AMR][1000 genomes]
rs49961	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1029145	chr5:57905821-58141221	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830311	chr5:57912546-58105636	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58027800-58049400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:58031000-58036000	Enhancers	Fetal Intestine Small	intestine
3	chr5:58031600-58036000	Enhancers	Fetal Intestine Large	intestine
4	chr5:58031800-58041400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:58033800-58034600	Flanking Active TSS	HepG2	liver
6	chr5:58034000-58034800	Enhancers	Liver	Liver
7	chr5:58034200-58035200	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr5:58034200-58035400	Enhancers	Stomach Mucosa	stomach
9	chr5:58034400-58035800	Weak transcription	Fetal Brain Male	brain

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