Variant report

Variant	rs4858824
Chromosome Location	chr3:47409616-47409617
allele	C/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:61)

rs_ID	r²[population]
rs1038394	1.00[CEU][hapmap]
rs1076394	0.96[CEU][hapmap]
rs10865946	1.00[CEU][hapmap]
rs11130123	0.92[CEU][hapmap]
rs11130124	0.96[CEU][hapmap]
rs11130126	0.88[CEU][hapmap]
rs11130128	1.00[CEU][hapmap]
rs11130129	1.00[CEU][hapmap]
rs11130137	1.00[CEU][hapmap]
rs11705957	1.00[CEU][hapmap]
rs11710013	0.96[CEU][hapmap]
rs11710121	0.88[CEU][hapmap]
rs11710322	0.96[CEU][hapmap]
rs11711265	1.00[CEU][hapmap]
rs11711824	1.00[CEU][hapmap]
rs11712445	1.00[CEU][hapmap]
rs11716763	1.00[CEU][hapmap]
rs11719877	1.00[CEU][hapmap]
rs11915074	0.89[CEU][hapmap]
rs11920853	0.89[CEU][hapmap]
rs12636851	1.00[CEU][hapmap]
rs13059519	1.00[CEU][hapmap]
rs13075233	1.00[CEU][hapmap]
rs13094438	0.96[CEU][hapmap]
rs1531875	1.00[CEU][hapmap]
rs1638676	0.96[CEU][hapmap]
rs17410853	0.88[CEU][hapmap]
rs17411375	0.96[CEU][hapmap]
rs17784882	1.00[CEU][hapmap]
rs1872164	1.00[CEU][hapmap]
rs2101247	0.96[CEU][hapmap]
rs2132173	0.84[CEU][hapmap]
rs2159400	0.96[CEU][hapmap]
rs2276853	0.96[CEU][hapmap]
rs2276854	0.96[CEU][hapmap]
rs2291298	1.00[CEU][hapmap]
rs295428	0.96[CEU][hapmap]
rs295441	0.96[CEU][hapmap]
rs295442	0.96[CEU][hapmap]
rs295449	0.96[CEU][hapmap]
rs295458	0.96[CEU][hapmap]
rs295461	0.96[CEU][hapmap]
rs3736177	1.00[CEU][hapmap]
rs3816779	1.00[CEU][hapmap]
rs4683326	0.96[CEU][hapmap]
rs4858811	1.00[CEU][hapmap]
rs4858868	1.00[CEU][hapmap]
rs4858893	1.00[CEU][hapmap]
rs4858894	0.92[CEU][hapmap]
rs6768221	0.88[CEU][hapmap]
rs6780013	0.92[CEU][hapmap]
rs6791842	0.96[CEU][hapmap]
rs6792461	1.00[CEU][hapmap]
rs6800271	1.00[CEU][hapmap]
rs7651762	1.00[CEU][hapmap]
rs807932	0.92[CEU][hapmap]
rs807936	0.96[CEU][hapmap]
rs811115	0.95[CEU][hapmap]
rs878659	1.00[CEU][hapmap]
rs922957	1.00[CEU][hapmap]
rs9683033	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
2	esv1807553	chr3:47393616-47470763	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv3802	chr3:47396674-47441951	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv235728	chr3:47409615-47409618	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4858824	RTP3	cis	lesional skin	skin_eQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47401600-47421200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:47404400-47411000	Weak transcription	Right Atrium	heart
3	chr3:47404600-47410000	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr3:47407400-47410000	Weak transcription	HepG2	liver
5	chr3:47407400-47412600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:47407600-47412200	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr3:47407600-47412600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:47407800-47412000	Weak transcription	Monocytes-CD14+_RO01746	blood

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