Variant report

Variant	rs28564901
Chromosome Location	chr5:54172102-54172103
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10042734	0.87[EUR][1000 genomes]
rs1005622	0.92[ASN][1000 genomes]
rs10056452	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10805469	0.83[EUR][1000 genomes]
rs10805470	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10940430	0.83[ASN][1000 genomes]
rs10940431	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10940432	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10940434	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11738151	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11742711	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11953607	0.83[ASN][1000 genomes]
rs12515327	0.82[EUR][1000 genomes]
rs12657845	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13181749	0.85[ASN][1000 genomes]
rs1560165	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1560166	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1560167	0.84[ASN][1000 genomes]
rs17588816	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1965716	0.84[EUR][1000 genomes]
rs2017082	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2019005	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2195392	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2195393	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2897758	0.86[EUR][1000 genomes]
rs3916738	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3935813	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4242047	0.83[EUR][1000 genomes]
rs4446420	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4502767	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4865879	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4865880	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4865881	0.84[ASN][1000 genomes]
rs4865882	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs734097	0.83[EUR][1000 genomes]
rs737526	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7709516	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs976645	0.86[EUR][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:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:54168600-54175600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:54170000-54178800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:54170200-54172400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:54170200-54172400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr5:54170600-54172400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:54170600-54172600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr5:54170800-54172400	Weak transcription	Fetal Intestine Small	intestine
8	chr5:54170800-54175800	Weak transcription	NHEK	skin
9	chr5:54171400-54172400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr5:54171400-54172400	Weak transcription	Pancreas	Pancrea
11	chr5:54171400-54172600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:54171400-54172600	Weak transcription	Stomach Mucosa	stomach
13	chr5:54171400-54172600	Weak transcription	Hela-S3	cervix
14	chr5:54171400-54172800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr5:54171400-54173000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:54171400-54176000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:54171800-54172200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr5:54171800-54172200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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