Variant report

Variant	rs56153390
Chromosome Location	chr5:178539149-178539150
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10036816	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10042855	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10060184	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10066739	1.00[AMR][1000 genomes]
rs10077338	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73806855	1.00[AMR][1000 genomes]
rs73806879	1.00[AMR][1000 genomes]
rs73806880	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73806883	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73806885	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73806886	1.00[AFR][1000 genomes];1.00[AMR][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	nsv1024560	chr5:178415364-178917595	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv537975	chr5:178415364-178917595	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv1033597	chr5:178423101-178752095	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1031829	chr5:178442633-178658706	Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv482750	chr5:178482653-178663586	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers 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	6 gene(s)	inside rSNPs	diseases
7	nsv1026790	chr5:178511268-178687428	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv482352	chr5:178525060-178697496	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 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	chr5:178527200-178540200	Weak transcription	HSMMtube	muscle
2	chr5:178527800-178559800	Weak transcription	HSMM	muscle
3	chr5:178538000-178544000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr5:178538000-178544400	ZNF genes & repeats	Liver	Liver
5	chr5:178538000-178550000	Strong transcription	Osteobl	bone
6	chr5:178538000-178560400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:178538200-178539200	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
8	chr5:178538200-178539800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr5:178538200-178564600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:178538400-178542800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:178538400-178544000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
12	chr5:178538600-178540400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:178538600-178542800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr5:178538600-178543600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:178538800-178539200	ZNF genes & repeats	Brain Hippocampus Middle	brain
16	chr5:178539000-178541600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
17	chr5:178539000-178543000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
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