Variant report

Variant	rs12474728
Chromosome Location	chr2:73086540-73086541
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:73051752..73054246-chr2:73085621..73088585,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144036	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10211019	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1027848	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865393	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126385	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11894160	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12622275	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12713775	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12989141	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13035731	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1567230	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995734	0.80[EUR][1000 genomes]
rs2048170	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2135985	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420880	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420881	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420883	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2421095	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4321391	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852893	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4852902	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546786	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546788	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546789	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546790	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546791	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546792	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6730083	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6739002	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6750740	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6758431	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6758542	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586787	0.91[EUR][1000 genomes]
rs7588602	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7592155	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs925146	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925147	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925148	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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	nsv834259	chr2:72941118-73114106	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12474728	CYP26B1	cis	Whole Blood	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73079000-73088200	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr2:73082200-73088200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:73082600-73088000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:73085000-73088200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:73085000-73089200	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links