Variant report

Variant	rs2562525
Chromosome Location	chr5:106746654-106746655
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs252803	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs252804	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs252805	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs252808	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs252810	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs252811	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs252812	0.95[EUR][1000 genomes]
rs252814	0.84[EUR][1000 genomes]
rs252815	0.84[EUR][1000 genomes]
rs252818	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs252819	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs252983	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs252984	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2731839	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2731840	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs431982	0.95[EUR][1000 genomes]
rs467472	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs468998	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030118	chr5:106006097-106847949	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1034276	chr5:106461538-106944163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv537851	chr5:106461538-106944163	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv34018	chr5:106720912-107110506	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 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	chr5:106732200-106753200	Weak transcription	Fetal Kidney	kidney
2	chr5:106738800-106761600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:106739000-106751200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:106739000-106754600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:106739000-106758200	Weak transcription	Left Ventricle	heart
6	chr5:106739600-106762600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:106740400-106749800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr5:106741000-106758200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:106741200-106749600	Weak transcription	A549	lung
10	chr5:106741200-106751600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:106742000-106753800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr5:106744200-106748000	Weak transcription	Fetal Heart	heart
13	chr5:106745000-106754000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:106745600-106751200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr5:106745600-106758400	Weak transcription	Right Ventricle	heart
16	chr5:106745600-106758400	Weak transcription	HMEC	breast
17	chr5:106745800-106753800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr5:106746600-106748400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:106746600-106753400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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