Variant report

Variant	rs4678442
Chromosome Location	chr3:136532971-136532972
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	chr3:136471469..136473912-chr3:136531466..136533756,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261758	Chromatin interaction

Extended variants
information (count: 198 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:195)

rs_ID	r²[population]
rs10470440	0.99[ASN][1000 genomes]
rs1052618	0.96[ASN][1000 genomes]
rs10935193	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10935198	0.99[ASN][1000 genomes]
rs10935199	0.84[EUR][1000 genomes]
rs10935210	0.90[ASN][1000 genomes]
rs11713817	0.93[AMR][1000 genomes]
rs11713867	0.88[AMR][1000 genomes]
rs11921170	0.84[ASN][1000 genomes]
rs11924477	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12330283	0.93[ASN][1000 genomes]
rs12486911	0.86[EUR][1000 genomes]
rs12487901	0.86[ASN][1000 genomes]
rs12488365	0.93[ASN][1000 genomes]
rs12491278	0.89[ASN][1000 genomes]
rs12491729	0.83[ASN][1000 genomes]
rs12491730	0.83[ASN][1000 genomes]
rs12497379	0.92[ASN][1000 genomes]
rs12630955	0.93[ASN][1000 genomes]
rs12633003	0.88[ASN][1000 genomes]
rs12637949	0.93[ASN][1000 genomes]
rs12695653	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs13315318	0.90[ASN][1000 genomes]
rs1344790	0.90[ASN][1000 genomes]
rs1347209	0.93[ASN][1000 genomes]
rs1400261	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1406540	0.99[ASN][1000 genomes]
rs1406541	0.99[ASN][1000 genomes]
rs1433318	0.88[ASN][1000 genomes]
rs1433319	0.88[ASN][1000 genomes]
rs1533445	0.90[ASN][1000 genomes]
rs1569228	0.99[ASN][1000 genomes]
rs1569229	0.99[ASN][1000 genomes]
rs17366234	0.85[EUR][1000 genomes]
rs1805300	0.96[ASN][1000 genomes]
rs1819095	0.93[ASN][1000 genomes]
rs1865149	0.93[ASN][1000 genomes]
rs1914048	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1965108	0.90[ASN][1000 genomes]
rs1965109	0.90[ASN][1000 genomes]
rs1971788	0.90[ASN][1000 genomes]
rs2031029	0.93[ASN][1000 genomes]
rs2031030	0.96[ASN][1000 genomes]
rs2031031	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2060303	0.96[ASN][1000 genomes]
rs2117009	0.93[ASN][1000 genomes]
rs2117010	0.93[ASN][1000 genomes]
rs2138540	0.93[ASN][1000 genomes]
rs2138541	0.89[ASN][1000 genomes]
rs2271684	0.99[ASN][1000 genomes]
rs2343663	0.93[ASN][1000 genomes]
rs28458819	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28671336	0.90[ASN][1000 genomes]
rs28672119	0.82[ASN][1000 genomes]
rs28761333	0.84[ASN][1000 genomes]
rs2880767	0.91[ASN][1000 genomes]
rs28877307	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35339486	0.93[ASN][1000 genomes]
rs35760633	0.90[ASN][1000 genomes]
rs3772387	0.90[ASN][1000 genomes]
rs3772388	0.90[ASN][1000 genomes]
rs3845925	0.88[ASN][1000 genomes]
rs3856623	0.90[ASN][1000 genomes]
rs3915455	0.89[ASN][1000 genomes]
rs3963921	0.90[ASN][1000 genomes]
rs4038076	0.96[ASN][1000 genomes]
rs4420814	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4533585	0.99[ASN][1000 genomes]
rs4600775	0.89[ASN][1000 genomes]
rs4678272	0.93[ASN][1000 genomes]
rs4678273	0.93[ASN][1000 genomes]
rs4678274	0.93[ASN][1000 genomes]
rs4678276	0.88[ASN][1000 genomes]
rs4678441	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4678443	0.99[ASN][1000 genomes]
rs4678444	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4678445	0.96[ASN][1000 genomes]
rs4678448	0.96[ASN][1000 genomes]
rs4678450	0.93[ASN][1000 genomes]
rs4678451	0.93[ASN][1000 genomes]
rs4678452	0.93[ASN][1000 genomes]
rs56163507	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56695781	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60574021	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6439663	0.99[ASN][1000 genomes]
rs6439664	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6439667	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6439670	0.88[ASN][1000 genomes]
rs6439671	0.96[ASN][1000 genomes]
rs6439672	0.96[ASN][1000 genomes]
rs6439673	0.93[ASN][1000 genomes]
rs6439675	0.93[ASN][1000 genomes]
rs6761993	0.93[ASN][1000 genomes]
rs6766755	0.97[ASN][1000 genomes]
rs6771717	0.90[ASN][1000 genomes]
rs6773117	0.99[ASN][1000 genomes]
rs6775389	0.88[ASN][1000 genomes]
rs6777816	0.96[ASN][1000 genomes]
rs67782618	0.86[EUR][1000 genomes]
rs6783508	0.92[ASN][1000 genomes]
rs6783999	0.90[ASN][1000 genomes]
rs6784005	0.93[ASN][1000 genomes]
rs6786302	0.90[ASN][1000 genomes]
rs6786648	0.93[ASN][1000 genomes]
rs6793936	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6793966	0.84[ASN][1000 genomes]
rs6797509	0.93[ASN][1000 genomes]
rs6800032	0.93[ASN][1000 genomes]
rs6800690	0.93[ASN][1000 genomes]
rs6802291	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6803618	0.93[ASN][1000 genomes]
rs6809943	0.95[ASN][1000 genomes]
rs7431100	0.90[ASN][1000 genomes]
rs7434143	0.93[ASN][1000 genomes]
rs7611847	0.90[ASN][1000 genomes]
rs7614422	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7617932	0.90[ASN][1000 genomes]
rs7621932	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7627443	0.96[ASN][1000 genomes]
rs7629659	0.81[ASN][1000 genomes]
rs7629882	0.93[ASN][1000 genomes]
rs7630571	0.99[ASN][1000 genomes]
rs7631017	0.90[ASN][1000 genomes]
rs7633629	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7639692	0.92[ASN][1000 genomes]
rs7645773	0.93[ASN][1000 genomes]
rs7647451	0.88[ASN][1000 genomes]
rs7648817	0.90[ASN][1000 genomes]
rs7651085	0.93[ASN][1000 genomes]
rs7651644	0.87[ASN][1000 genomes]
rs835649	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs856662	0.85[ASN][1000 genomes]
rs9289518	0.93[ASN][1000 genomes]
rs9289519	0.93[ASN][1000 genomes]
rs9289520	0.96[ASN][1000 genomes]
rs9289523	0.93[ASN][1000 genomes]
rs938524	0.93[ASN][1000 genomes]
rs938525	0.96[ASN][1000 genomes]
rs9682106	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9757179	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9811169	0.93[ASN][1000 genomes]
rs9815771	0.93[ASN][1000 genomes]
rs9817453	0.96[ASN][1000 genomes]
rs9817967	0.93[ASN][1000 genomes]
rs9818397	0.99[ASN][1000 genomes]
rs9818792	0.93[ASN][1000 genomes]
rs9819572	0.99[ASN][1000 genomes]
rs9819743	0.99[ASN][1000 genomes]
rs9821557	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9823565	0.99[ASN][1000 genomes]
rs9827648	0.96[ASN][1000 genomes]
rs9828009	0.93[ASN][1000 genomes]
rs9832045	0.99[ASN][1000 genomes]
rs9833952	0.88[ASN][1000 genomes]
rs9834250	0.99[ASN][1000 genomes]
rs9834438	0.93[ASN][1000 genomes]
rs9834861	0.93[ASN][1000 genomes]
rs9835096	0.99[ASN][1000 genomes]
rs9836807	0.96[ASN][1000 genomes]
rs9837990	0.93[ASN][1000 genomes]
rs9838022	0.93[ASN][1000 genomes]
rs9841985	0.88[ASN][1000 genomes]
rs9842145	0.90[ASN][1000 genomes]
rs9842436	0.93[ASN][1000 genomes]
rs9842577	0.99[ASN][1000 genomes]
rs9843352	0.99[ASN][1000 genomes]
rs9843733	0.93[ASN][1000 genomes]
rs9846334	0.93[ASN][1000 genomes]
rs9846691	0.93[ASN][1000 genomes]
rs9846754	0.88[ASN][1000 genomes]
rs9847548	0.99[ASN][1000 genomes]
rs9848867	0.93[ASN][1000 genomes]
rs9849767	0.99[ASN][1000 genomes]
rs9851726	0.90[ASN][1000 genomes]
rs9853417	0.93[ASN][1000 genomes]
rs9855314	0.93[ASN][1000 genomes]
rs9856828	0.93[ASN][1000 genomes]
rs9859665	0.93[ASN][1000 genomes]
rs9859810	0.93[ASN][1000 genomes]
rs9860774	0.99[ASN][1000 genomes]
rs9863551	0.89[ASN][1000 genomes]
rs9864926	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9864941	0.90[ASN][1000 genomes]
rs9865545	0.96[ASN][1000 genomes]
rs9870377	0.94[ASN][1000 genomes]
rs9871987	0.88[ASN][1000 genomes]
rs9874887	0.93[ASN][1000 genomes]
rs9878031	0.92[ASN][1000 genomes]
rs9878117	0.93[ASN][1000 genomes]
rs9878367	0.93[ASN][1000 genomes]
rs9878464	0.93[ASN][1000 genomes]
rs9880708	0.92[ASN][1000 genomes]
rs9881139	0.93[ASN][1000 genomes]
rs9883131	0.93[ASN][1000 genomes]
rs9883979	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877530	chr3:136514310-136604697	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	n/a
2	nsv877531	chr3:136517016-136662954	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv877532	chr3:136526939-136662603	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4678442	PCCB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136531000-136535400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr3:136531000-136535800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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