Variant report

Variant	rs1901554
Chromosome Location	chr3:56256543-56256544
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10433621	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1078309	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1078310	0.88[ASN][1000 genomes]
rs11926826	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12486948	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12490280	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12492055	0.91[ASN][1000 genomes]
rs12492253	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12635356	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1376984	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1452214	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1452217	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1452218	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1564907	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1586314	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1601451	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17056646	0.91[ASN][1000 genomes]
rs17732598	0.88[ASN][1000 genomes]
rs1825560	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2316477	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2316478	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2316480	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35431468	1.00[ASN][1000 genomes]
rs4425224	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4974120	0.88[ASN][1000 genomes]
rs4974121	0.89[ASN][1000 genomes]
rs4974123	0.86[ASN][1000 genomes]
rs4974175	0.81[AMR][1000 genomes]
rs4974176	0.88[ASN][1000 genomes]
rs4974179	0.91[ASN][1000 genomes]
rs4974180	0.88[ASN][1000 genomes]
rs55849756	0.91[ASN][1000 genomes]
rs59079055	0.94[ASN][1000 genomes]
rs60383545	0.89[ASN][1000 genomes]
rs6445768	0.95[EUR][1000 genomes]
rs6445770	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6779122	0.81[AMR][1000 genomes]
rs6782034	0.88[ASN][1000 genomes]
rs6783356	0.91[ASN][1000 genomes]
rs6786058	0.91[ASN][1000 genomes]
rs6787104	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6801342	0.91[ASN][1000 genomes]
rs6803165	0.89[ASN][1000 genomes]
rs755321	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7613726	0.91[ASN][1000 genomes]
rs7636352	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7644153	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7644257	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7650293	0.92[ASN][1000 genomes]
rs965961	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs977313	1.00[ASN][1000 genomes]
rs9877547	0.83[AMR][1000 genomes];0.97[EUR][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	nsv1009709	chr3:56000827-56294945	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr3:56252000-56272200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:56254800-56256600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:56254800-56257000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:56254800-56257000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:56254800-56258200	Weak transcription	Brain Angular Gyrus	brain
6	chr3:56254800-56280600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:56255000-56257000	Weak transcription	Brain Substantia Nigra	brain
8	chr3:56256400-56257600	Enhancers	Brain Hippocampus Middle	brain
9	chr3:56256400-56258200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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