Variant report

Variant	rs12509066
Chromosome Location	chr4:69792818-69792819
allele	C/T
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	KAP1	chr4:69792807-69793420	U2OS	brain:	n/a	n/a
2	FOXP2	chr4:69792745-69793190	SK-N-MC	brain:	n/a	chr4:69792871-69792883 chr4:69792867-69792879
3	POLR2A	chr4:69792764-69793302	SK-N-MC	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000198277	TF binding region

Extended variants
information (count: 120 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10000598	0.81[EUR][1000 genomes]
rs10001065	0.92[EUR][1000 genomes]
rs10006282	0.81[EUR][1000 genomes]
rs10010699	0.81[EUR][1000 genomes]
rs10013724	0.92[EUR][1000 genomes]
rs10024664	0.92[EUR][1000 genomes]
rs10032748	0.91[EUR][1000 genomes]
rs1020767	0.88[EUR][1000 genomes]
rs10518057	0.81[EUR][1000 genomes]
rs10903220	0.92[EUR][1000 genomes]
rs10903221	0.92[EUR][1000 genomes]
rs10903224	0.81[EUR][1000 genomes]
rs11249512	0.90[EUR][1000 genomes]
rs11249513	0.90[EUR][1000 genomes]
rs11249515	0.90[EUR][1000 genomes]
rs1159714	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1159715	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11736796	0.91[EUR][1000 genomes]
rs11931604	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs11932983	0.83[EUR][1000 genomes]
rs11936412	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11937195	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs11940320	0.89[EUR][1000 genomes]
rs11945620	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs11946857	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11946976	0.83[EUR][1000 genomes]
rs12499093	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12500933	0.87[EUR][1000 genomes]
rs12506592	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs12507556	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs12508920	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12509040	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12510036	0.89[EUR][1000 genomes]
rs13104293	0.87[EUR][1000 genomes]
rs13106664	0.89[EUR][1000 genomes]
rs13113544	0.86[EUR][1000 genomes]
rs13128286	0.91[EUR][1000 genomes]
rs13128843	0.92[EUR][1000 genomes]
rs13132528	0.81[EUR][1000 genomes]
rs13148179	0.83[EUR][1000 genomes]
rs13148603	0.81[EUR][1000 genomes]
rs1379813	0.81[EUR][1000 genomes]
rs1379816	0.81[EUR][1000 genomes]
rs1458236	0.90[EUR][1000 genomes]
rs1458237	0.91[EUR][1000 genomes]
rs1458242	0.85[EUR][1000 genomes]
rs1458243	0.80[EUR][1000 genomes]
rs1458245	0.81[EUR][1000 genomes]
rs1458246	0.81[EUR][1000 genomes]
rs1598904	0.81[EUR][1000 genomes]
rs17146967	0.87[EUR][1000 genomes]
rs17605102	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1841037	0.87[EUR][1000 genomes]
rs1902925	0.92[EUR][1000 genomes]
rs1902926	0.92[EUR][1000 genomes]
rs1902927	0.92[EUR][1000 genomes]
rs1902928	0.92[EUR][1000 genomes]
rs1962953	0.92[EUR][1000 genomes]
rs1968764	0.84[EUR][1000 genomes]
rs1989329	0.82[EUR][1000 genomes]
rs1993546	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1993547	0.86[EUR][1000 genomes]
rs2009312	0.92[EUR][1000 genomes]
rs2017125	0.92[EUR][1000 genomes]
rs2018150	0.92[EUR][1000 genomes]
rs2125305	0.92[EUR][1000 genomes]
rs2125307	0.81[EUR][1000 genomes]
rs2168840	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2168841	0.90[EUR][1000 genomes]
rs2331561	0.90[EUR][1000 genomes]
rs2331562	0.90[EUR][1000 genomes]
rs2331577	0.91[EUR][1000 genomes]
rs3088249	0.92[EUR][1000 genomes]
rs3749511	0.91[EUR][1000 genomes]
rs3749513	0.92[EUR][1000 genomes]
rs3828504	0.91[EUR][1000 genomes]
rs4343788	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs4412056	0.91[EUR][1000 genomes]
rs4434329	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4518317	0.92[EUR][1000 genomes]
rs4694358	0.88[EUR][1000 genomes]
rs4694389	0.87[EUR][1000 genomes]
rs4694448	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4694449	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55647928	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55795005	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55831171	0.83[EUR][1000 genomes]
rs56371633	0.87[EUR][1000 genomes]
rs56943005	0.83[EUR][1000 genomes]
rs60276248	0.83[EUR][1000 genomes]
rs6600857	0.92[EUR][1000 genomes]
rs6842605	0.87[EUR][1000 genomes]
rs6843537	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843550	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847539	0.93[EUR][1000 genomes]
rs6849125	0.89[EUR][1000 genomes]
rs6858791	0.83[EUR][1000 genomes]
rs7435335	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs7441753	0.81[EUR][1000 genomes]
rs7666446	0.92[EUR][1000 genomes]
rs7674475	0.92[EUR][1000 genomes]
rs7680341	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7692753	0.82[EUR][1000 genomes]
rs9329037	0.80[EUR][1000 genomes]
rs969338	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs994229	0.92[EUR][1000 genomes]
rs9991142	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9996467	0.92[EUR][1000 genomes]
rs9999996	0.92[EUR][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	nsv4372	chr4:69764499-69810115	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	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
11	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12509066	UGT2B7	cis	multi-tissue	Pritchard

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69790600-69793800	Weak transcription	HepG2	liver
2	chr4:69791800-69794800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:69792000-69795000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr4:69792400-69812600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:69792800-69793000	ZNF genes & repeats	Fetal Intestine Large	intestine
6	chr4:69792800-69793200	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr4:69792800-69793400	Enhancers	Liver	Liver

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