Variant report

Variant	rs4858856
Chromosome Location	chr3:47565424-47565425
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47564010..47565743-chr3:47604722..47606616,2	MCF-7	breast:
2	chr3:47564092..47565770-chr3:47566489..47568024,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1038394	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs10865946	1.00[CEU][hapmap]
rs11130128	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11130129	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11130132	0.95[EUR][1000 genomes]
rs11130133	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130137	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11705957	1.00[CEU][hapmap]
rs11707895	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11711265	1.00[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711824	1.00[CEU][hapmap]
rs11712445	1.00[CEU][hapmap]
rs11713413	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11716763	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11719877	1.00[CEU][hapmap]
rs11914795	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11914913	0.93[EUR][1000 genomes]
rs11914932	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12489046	0.89[EUR][1000 genomes]
rs12490058	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12492433	0.89[EUR][1000 genomes]
rs12630641	0.92[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12636851	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs13059519	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs13075233	1.00[CEU][hapmap]
rs1531875	1.00[CEU][hapmap]
rs1564760	0.91[ASN][1000 genomes]
rs1564761	0.95[ASN][1000 genomes]
rs17411375	0.96[CEU][hapmap]
rs17784882	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1872164	1.00[CEU][hapmap]
rs1872166	0.95[ASN][1000 genomes]
rs2101247	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs2159400	0.96[CEU][hapmap]
rs2291298	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs295449	0.96[CEU][hapmap]
rs295458	0.96[CEU][hapmap]
rs295461	0.96[CEU][hapmap]
rs34634681	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3736177	1.00[CEU][hapmap]
rs3816779	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4599332	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4858811	1.00[CEU][hapmap]
rs4858824	1.00[CEU][hapmap]
rs4858868	1.00[CEU][hapmap]
rs4858893	1.00[CEU][hapmap]
rs4858894	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs59586735	0.89[EUR][1000 genomes]
rs60369822	0.84[EUR][1000 genomes]
rs62248599	0.88[EUR][1000 genomes]
rs62248603	0.84[EUR][1000 genomes]
rs62248605	0.90[EUR][1000 genomes]
rs62260710	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260711	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260741	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6765990	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs6768879	0.88[ASN][1000 genomes]
rs6780013	0.92[CEU][hapmap]
rs6790763	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6792461	1.00[CEU][hapmap]
rs6792488	0.86[EUR][1000 genomes]
rs6800271	1.00[CEU][hapmap]
rs73081205	0.87[EUR][1000 genomes]
rs7628631	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649234	0.86[EUR][1000 genomes]
rs7651194	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7651762	1.00[CEU][hapmap]
rs878659	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs922957	1.00[CEU][hapmap]
rs9683033	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9683177	0.86[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	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4858856	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs4858856	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47555600-47568200	Weak transcription	Right Atrium	heart
2	chr3:47564000-47566200	Weak transcription	Fetal Thymus	thymus
3	chr3:47564200-47568000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:47564200-47569600	Weak transcription	NHEK	skin
5	chr3:47564400-47566200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:47564400-47569400	Weak transcription	HMEC	breast
7	chr3:47564600-47566600	Enhancers	HepG2	liver
8	chr3:47564600-47567200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:47565200-47569600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:47565200-47574800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:47565400-47565600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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