Variant report

Variant	rs2407758
Chromosome Location	chr5:54186701-54186702
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10044930	0.92[ASN][1000 genomes]
rs1005622	0.87[CEU][hapmap];0.90[GIH][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs13161386	0.81[EUR][1000 genomes]
rs13161718	0.81[EUR][1000 genomes]
rs1560167	0.87[CEU][hapmap];0.90[GIH][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs1965716	0.94[ASN][1000 genomes]
rs1988528	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1991498	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2017318	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2017540	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2897758	0.99[ASN][1000 genomes]
rs4074332	0.82[GIH][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap]
rs4315891	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4320216	0.87[CEU][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap]
rs4373237	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4407587	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4446420	0.85[ASN][1000 genomes]
rs4865586	0.85[CEU][hapmap];0.80[CHB][hapmap];0.80[CHD][hapmap];0.94[GIH][hapmap];0.87[JPT][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4865587	0.85[ASN][1000 genomes]
rs4865881	0.81[EUR][1000 genomes]
rs4865883	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6860824	0.85[CEU][hapmap];0.94[GIH][hapmap];0.87[JPT][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs6893903	0.90[EUR][1000 genomes]
rs734097	0.98[ASN][1000 genomes]
rs7708368	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7734613	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs976645	0.95[ASN][1000 genomes]
rs981978	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:54180400-54187800	Weak transcription	Gastric	stomach
2	chr5:54185200-54186800	Enhancers	Hela-S3	cervix
3	chr5:54185200-54186800	Enhancers	HSMMtube	muscle
4	chr5:54186200-54196600	Weak transcription	Fetal Muscle Leg	muscle
5	chr5:54186400-54186800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr5:54186400-54191200	Weak transcription	Fetal Kidney	kidney
7	chr5:54186600-54190800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:54186600-54190800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr5:54186600-54191000	Weak transcription	HSMM	muscle

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