Variant report

Variant	rs4864451
Chromosome Location	chr4:54123785-54123786
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10013573	0.86[CHB][hapmap]
rs10517291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10517292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10517296	0.85[CHB][hapmap]
rs11133267	0.85[CHB][hapmap]
rs11929903	0.93[CHB][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11930070	1.00[CEU][hapmap]
rs11939189	0.93[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs11947322	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11947928	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12108246	0.93[CHB][hapmap];0.81[JPT][hapmap];0.94[YRI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12499016	0.86[CHB][hapmap]
rs12499731	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12500564	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12505661	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12507228	0.82[ASN][1000 genomes]
rs12512748	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13120051	0.86[CHB][hapmap]
rs1351514	0.85[CHB][hapmap]
rs17082453	0.85[CHB][hapmap]
rs17082476	0.93[CHB][hapmap]
rs17082504	0.93[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17082529	0.82[ASN][1000 genomes]
rs17082549	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17082565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17082579	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs17082581	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1987028	0.93[CHB][hapmap];0.82[JPT][hapmap]
rs2001881	0.85[CHB][hapmap]
rs2128103	0.85[CHB][hapmap]
rs34019927	0.82[AMR][1000 genomes]
rs35225781	0.85[CHB][hapmap]
rs35784764	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3817270	0.86[CHB][hapmap]
rs4299650	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4385131	1.00[CEU][hapmap];0.92[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4419530	0.85[AMR][1000 genomes]
rs4421047	0.93[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes]
rs4529117	0.85[AMR][1000 genomes]
rs4864452	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4864453	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4864454	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4864747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4864753	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6420001	0.85[CHB][hapmap]
rs6554096	0.86[CHB][hapmap]
rs6826467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6830879	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6854446	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72498838	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73147378	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73147396	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73149212	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs751265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7664488	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7664645	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7684450	0.86[CHB][hapmap]
rs7687029	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7688646	0.93[CHB][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7696426	0.85[CHB][hapmap]
rs9762074	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9992820	0.85[CHB][hapmap]

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	nsv997614	chr4:54086727-54150632	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv879013	chr4:54093717-54137228	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1008593	chr4:54120297-54207769	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4864451	SCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54101600-54129400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr4:54108400-54129600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr4:54114400-54134400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:54114400-54139600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:54114400-54144000	Weak transcription	Liver	Liver
6	chr4:54114600-54126400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr4:54114600-54129800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:54114800-54129400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:54114800-54130000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr4:54117800-54132800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr4:54119600-54130400	Weak transcription	NHLF	lung
12	chr4:54120600-54124000	Weak transcription	Primary T cells from cord blood	blood
13	chr4:54122200-54139800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr4:54122600-54127400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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