Variant report

Variant	rs17078820
Chromosome Location	chr5:178397022-178397023
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10067521	0.81[JPT][hapmap]
rs1046726	0.85[JPT][hapmap]
rs10479515	0.81[JPT][hapmap]
rs10479516	0.81[JPT][hapmap]
rs10516152	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11743869	0.81[JPT][hapmap]
rs12186577	0.92[JPT][hapmap]
rs12652581	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12652691	0.83[JPT][hapmap]
rs12653128	0.83[JPT][hapmap]
rs12654454	0.85[JPT][hapmap]
rs12654770	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12654969	0.85[JPT][hapmap]
rs17078817	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17078829	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17078837	0.91[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs17078848	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17078852	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17078853	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17078862	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17078872	0.94[ASN][1000 genomes]
rs17078877	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17078880	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17078888	0.94[ASN][1000 genomes]
rs2071249	0.91[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2645341	0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3733915	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58018977	1.00[AMR][1000 genomes]
rs58175257	0.92[ASN][1000 genomes]
rs58473745	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58533505	0.97[ASN][1000 genomes]
rs59987112	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61200088	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61565874	0.92[ASN][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	nsv600489	chr5:178368096-178430375	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1017941	chr5:178384214-178427401	ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv537974	chr5:178384214-178427401	ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv883219	chr5:178390237-178454118	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv883220	chr5:178394717-178454118	ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178369400-178418200	ZNF genes & repeats	Fetal Brain Female	brain
2	chr5:178388800-178398600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr5:178389000-178398200	ZNF genes & repeats	Brain Hippocampus Middle	brain
4	chr5:178389200-178398400	ZNF genes & repeats	Liver	Liver
5	chr5:178389400-178400400	ZNF genes & repeats	Adipose Nuclei	Adipose
6	chr5:178389400-178405200	ZNF genes & repeats	Brain Germinal Matrix	brain
7	chr5:178389800-178398400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
8	chr5:178389800-178399600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:178389800-178400000	ZNF genes & repeats	Fetal Stomach	stomach
10	chr5:178394800-178398400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
11	chr5:178395200-178397800	ZNF genes & repeats	Stomach Smooth Muscle	stomach
12	chr5:178395600-178400200	ZNF genes & repeats	Fetal Lung	lung
13	chr5:178395800-178398200	ZNF genes & repeats	Fetal Brain Male	brain
14	chr5:178396000-178398600	ZNF genes & repeats	Left Ventricle	heart
15	chr5:178396000-178402400	Weak transcription	Fetal Heart	heart
16	chr5:178396200-178398800	ZNF genes & repeats	Aorta	Aorta
17	chr5:178396600-178397200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
18	chr5:178396800-178400200	ZNF genes & repeats	Ovary	ovary
19	chr5:178397000-178397400	ZNF genes & repeats	Right Ventricle	heart

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