Variant report

Variant	rs2017540
Chromosome Location	chr5:54176976-54176977
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10044930	0.87[ASN][1000 genomes]
rs1005622	0.81[EUR][1000 genomes]
rs13161386	0.81[EUR][1000 genomes]
rs13161718	0.81[EUR][1000 genomes]
rs1560167	0.81[EUR][1000 genomes]
rs1965716	1.00[ASN][1000 genomes]
rs1988528	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1991498	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2017318	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407758	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2897758	0.95[ASN][1000 genomes]
rs4074332	0.80[ASN][1000 genomes]
rs4315891	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4373237	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4407587	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4446420	0.87[ASN][1000 genomes]
rs4865586	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4865587	0.87[ASN][1000 genomes]
rs4865881	0.81[EUR][1000 genomes]
rs4865883	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6860824	0.95[EUR][1000 genomes]
rs6893903	0.90[EUR][1000 genomes]
rs734097	0.94[ASN][1000 genomes]
rs7708368	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7734613	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs976645	0.92[ASN][1000 genomes]
rs981978	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][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	nsv830300	chr5:54056300-54257344	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv3358092	chr5:54077828-54189150	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv598179	chr5:54156269-54192823	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:54170000-54178800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:54173200-54178800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:54174400-54179000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:54174600-54177000	Weak transcription	Osteobl	bone
5	chr5:54174800-54178600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:54175800-54177000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:54175800-54177000	Enhancers	NHEK	skin
8	chr5:54176000-54179200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr5:54176000-54179200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:54176200-54178200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr5:54176600-54178400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:54176600-54179200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:54176800-54178600	Enhancers	HMEC	breast

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