Variant report

Variant	rs1458246
Chromosome Location	chr4:69818082-69818083
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr4:69817993-69818138	HepG2	liver:	n/a	chr4:69818070-69818081
2	NFIC	chr4:69816915-69818286	HepG2	liver:	n/a	n/a
3	TBP	chr4:69816831-69818180	HepG2	liver:	n/a	n/a
4	FOXA1	chr4:69817024-69818124	HepG2	liver:	n/a	n/a
5	MAX	chr4:69817096-69818126	HepG2	liver:	n/a	n/a
6	CEBPB	chr4:69817147-69818247	HepG2	liver:	n/a	chr4:69818070-69818081
7	ARID3A	chr4:69816858-69818218	HepG2	liver:	n/a	n/a
8	TCF7L2	chr4:69817279-69818089	HepG2	liver:	n/a	n/a
9	CEBPB	chr4:69817908-69818225	IMR90	lung:	n/a	chr4:69818070-69818081

Variant related genes	Relation type
UGT2A3	TF binding region

Extended variants
information (count: 117 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10000598	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10001065	0.89[EUR][1000 genomes]
rs10006282	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10010699	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10013724	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10024664	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10032748	0.88[EUR][1000 genomes]
rs1020767	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10518057	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10903220	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10903221	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10903224	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11249512	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11249513	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11249515	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1159714	0.83[EUR][1000 genomes]
rs1159715	0.83[EUR][1000 genomes]
rs11736796	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11931604	0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs11932983	0.84[EUR][1000 genomes]
rs11936412	0.89[EUR][1000 genomes]
rs11937195	0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs11945620	0.80[EUR][1000 genomes]
rs11946857	0.81[EUR][1000 genomes]
rs11946976	0.84[EUR][1000 genomes]
rs12499093	0.89[EUR][1000 genomes]
rs12499192	0.80[EUR][1000 genomes]
rs12506592	0.86[TSI][hapmap]
rs12507173	0.80[EUR][1000 genomes]
rs12507556	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs12508596	0.80[EUR][1000 genomes]
rs12508920	0.89[EUR][1000 genomes]
rs12509040	0.91[EUR][1000 genomes]
rs12509066	0.81[EUR][1000 genomes]
rs13104293	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13106664	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13113544	0.83[EUR][1000 genomes]
rs13128286	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13128843	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13132528	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13148179	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13148603	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1379813	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1379814	0.90[AFR][1000 genomes]
rs1379816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1458236	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1458237	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1458242	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1458243	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1458245	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1598904	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17605102	0.92[EUR][1000 genomes]
rs1841036	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1902925	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1902926	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1902927	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1902928	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1962953	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1993546	0.89[EUR][1000 genomes]
rs1993547	0.83[EUR][1000 genomes]
rs2009312	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2017125	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2018150	0.89[EUR][1000 genomes]
rs2125305	0.89[EUR][1000 genomes]
rs2125307	0.82[EUR][1000 genomes]
rs2168840	0.81[EUR][1000 genomes]
rs2168841	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2331561	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2331562	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2331577	0.88[EUR][1000 genomes]
rs3088249	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3749511	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3749513	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3828504	0.88[EUR][1000 genomes]
rs4343788	0.80[EUR][1000 genomes]
rs4412056	0.88[EUR][1000 genomes]
rs4418041	0.82[EUR][1000 genomes]
rs4518317	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4554146	0.80[EUR][1000 genomes]
rs4579191	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4694152	0.81[EUR][1000 genomes]
rs4694448	0.83[EUR][1000 genomes]
rs4694449	0.83[EUR][1000 genomes]
rs4694550	0.82[EUR][1000 genomes]
rs4694606	0.80[EUR][1000 genomes]
rs55647928	0.81[EUR][1000 genomes]
rs55795005	0.81[EUR][1000 genomes]
rs55831171	0.84[EUR][1000 genomes]
rs56943005	0.84[EUR][1000 genomes]
rs57468707	0.81[EUR][1000 genomes]
rs59732068	0.81[EUR][1000 genomes]
rs60276248	0.84[EUR][1000 genomes]
rs6600857	0.89[EUR][1000 genomes]
rs6843550	0.81[EUR][1000 genomes]
rs72642938	0.82[EUR][1000 genomes]
rs72642947	0.82[EUR][1000 genomes]
rs7435335	0.86[TSI][hapmap]
rs7441753	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7666446	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7674475	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7692753	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9329037	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs969338	0.83[EUR][1000 genomes]
rs994229	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9996467	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9999996	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005513	chr4:69446718-69890307	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv999654	chr4:69661415-70132110	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	esv3420586	chr4:69680878-70322918	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	esv3398036	chr4:69700493-69841391	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1067773	chr4:69718248-70715727	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	esv3468151	chr4:69718675-70322776	Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
7	esv3468153	chr4:69718675-70322776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv436447	chr4:69743339-69851390	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv967758	chr4:69780530-69870183	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv829962	chr4:69786869-69910283	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv10519	chr4:69816500-69835939	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1458246	C4orf7	cis	cerebellum	SCAN
rs1458246	UGT2B7	cis	multi-tissue	Pritchard

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69808600-69819600	Weak transcription	Small Intestine	intestine
2	chr4:69815200-69825600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:69817200-69819800	Enhancers	HepG2	liver
4	chr4:69817400-69819600	Weak transcription	Pancreas	Pancrea
5	chr4:69817600-69818200	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr4:69817600-69818600	Enhancers	Liver	Liver
7	chr4:69817600-69818600	Weak transcription	Fetal Heart	heart
8	chr4:69817600-69818600	Weak transcription	Stomach Mucosa	stomach
9	chr4:69817600-69820600	Enhancers	Fetal Intestine Large	intestine
10	chr4:69817600-69820600	Enhancers	Fetal Intestine Small	intestine
11	chr4:69817800-69820400	Enhancers	Duodenum Mucosa	Duodenum
12	chr4:69818000-69818200	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr4:69818000-69818600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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