Variant report

Variant	rs4801996
Chromosome Location	chr19:39471990-39471991
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39469273..39472050-chr19:39495885..39497816,2	MCF-7	breast:
2	chr19:39470454..39473191-chr19:39473840..39476726,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10403486	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10408493	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10415667	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10417436	0.82[CEU][hapmap]
rs11667641	0.82[CEU][hapmap]
rs11883422	0.83[CEU][hapmap]
rs12461981	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12608659	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12609806	0.82[CEU][hapmap]
rs1654334	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1840745	0.82[CEU][hapmap]
rs1840748	0.82[CEU][hapmap]
rs2318464	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2318465	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2318956	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28378068	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34638406	0.86[ASN][1000 genomes]
rs3848622	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803193	0.81[CEU][hapmap]
rs490761	0.87[EUR][1000 genomes]
rs55722117	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57214361	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57810919	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs581978	0.95[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58762231	0.82[ASN][1000 genomes]
rs59268123	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs606372	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61265620	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs622528	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs637972	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs638015	0.89[EUR][1000 genomes]
rs649150	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs650027	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6508843	0.83[CEU][hapmap]
rs7249004	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7250349	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7251721	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7251820	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7258123	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7258386	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7259801	0.82[CEU][hapmap]
rs72623864	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7508413	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8104751	0.82[CEU][hapmap]
rs8105165	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8105298	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4801996	FBXO27	cis	Skin Sun Exposed Lower leg	GTEx
rs4801996	CTB-189B5.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39470400-39472000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:39471200-39472000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
3	chr19:39471400-39472000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
4	chr19:39471400-39472200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr19:39471400-39472200	Flanking Active TSS	HepG2	liver
6	chr19:39471400-39472800	Enhancers	Liver	Liver
7	chr19:39471800-39472000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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