Variant report

Variant	rs4788810
Chromosome Location	chr16:71621637-71621638
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71598017..71601337-chr16:71621036..71625062,4	MCF-7	breast:
2	chr16:71619005..71622158-chr16:71624497..71628582,3	MCF-7	breast:
3	chr16:71620059..71623986-chr16:71624555..71628126,4	K562	blood:

Variant related genes	Relation type
ENSG00000260886	Chromatin interaction
ENSG00000157429	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs1058750	1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10852502	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10852503	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075893	0.82[EUR][1000 genomes]
rs11075894	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075898	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075901	0.90[CEU][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs11075904	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs11862723	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12929547	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1364210	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1392484	1.00[ASN][1000 genomes]
rs1423983	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032918	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052584	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052585	0.85[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2113223	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2133773	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2247603	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2334880	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4354946	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788548	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788550	1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788553	1.00[ASN][1000 genomes]
rs4788557	1.00[ASN][1000 genomes]
rs4788813	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788820	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788822	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788823	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788828	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4788830	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499526	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499527	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499528	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499529	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499530	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499531	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6499534	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6499538	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6499540	1.00[ASN][1000 genomes]
rs7186112	1.00[ASN][1000 genomes]
rs7187948	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7188675	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7190487	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7193549	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7195059	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7202479	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7204608	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7204967	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7204992	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7206470	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7359478	1.00[ASN][1000 genomes]
rs8044144	0.83[ASN][1000 genomes]
rs8051968	1.00[ASN][1000 genomes]
rs8052152	1.00[LWK][hapmap]
rs8052910	1.00[ASN][1000 genomes]
rs8053186	1.00[ASN][1000 genomes]
rs8053745	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8058297	0.85[EUR][1000 genomes]
rs8062188	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs889568	1.00[ASN][1000 genomes]
rs9635524	1.00[ASN][1000 genomes]
rs979790	1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9888756	1.00[ASN][1000 genomes]
rs9929840	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes]
rs9929985	1.00[ASN][1000 genomes]
rs9930015	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs9931074	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9934301	0.85[CEU][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9937511	1.00[ASN][1000 genomes]
rs9939458	0.81[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1063338	chr16:71612346-71752968	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4788810	PHLPP2	cis	Muscle Skeletal	GTEx
rs4788810	NRN1L	cis	parietal	SCAN
rs4788810	COG4	cis	parietal	SCAN
rs4788810	PHLPPL	cis	multi-tissue	Pritchard
rs4788810	B3GNT9	cis	parietal	SCAN
rs4788810	CBFB	cis	parietal	SCAN
rs4788810	RANBP10	cis	parietal	SCAN
rs4788810	ZNF23	cis	parietal	SCAN
rs4788810	MARVELD3	cis	Skin Sun Exposed Lower leg	GTEx
rs4788810	RP11-510M2.10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71619400-71621800	Enhancers	HepG2	liver
2	chr16:71620200-71624200	Weak transcription	Liver	Liver
3	chr16:71621200-71622000	Bivalent Enhancer	Primary B cells from peripheral blood	blood

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