Variant report

Variant	rs2018150
Chromosome Location	chr4:69778706-69778707
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	FOXA1	chr4:69778543-69778888	HepG2	liver:	n/a	n/a
2	GATA3	chr4:69778379-69778832	MCF-7	breast:	n/a	n/a
3	GATA3	chr4:69778166-69778902	MCF-7	breast:	n/a	n/a
4	EP300	chr4:69778450-69778856	MCF-7	breast:	n/a	n/a
5	FOSL2	chr4:69778565-69778944	A549	lung:	n/a	n/a
6	TCF7L2	chr4:69778499-69778821	MCF-7	breast:	n/a	n/a
7	GATA3	chr4:69778323-69778920	MCF-7	breast:	n/a	n/a
8	TCF12	chr4:69778363-69779057	A549	lung:	n/a	n/a
9	EP300	chr4:69778403-69779001	A549	lung:	n/a	n/a
10	ZNF217	chr4:69778446-69778741	MCF-7	breast:	n/a	n/a
11	FOXA2	chr4:69778617-69778830	HepG2	liver:	n/a	n/a
12	FOXA1	chr4:69778470-69778934	HepG2	liver:	n/a	n/a
13	GATA3	chr4:69778317-69779086	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:69770351..69773308-chr4:69775332..69780038,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249985	TF binding region
ENSG00000272626	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10000598	0.89[EUR][1000 genomes]
rs10000974	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10001065	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10004381	0.84[AFR][1000 genomes]
rs10006282	0.89[EUR][1000 genomes]
rs10010699	0.89[EUR][1000 genomes]
rs10013724	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10024664	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10032748	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1020767	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1020768	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10518057	0.89[EUR][1000 genomes]
rs10903220	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10903221	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10903224	0.89[EUR][1000 genomes]
rs11249512	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11249513	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11249515	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1159714	0.90[EUR][1000 genomes]
rs1159715	0.90[EUR][1000 genomes]
rs11736796	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11931604	0.86[TSI][hapmap]
rs11936412	0.82[EUR][1000 genomes]
rs11937195	0.86[TSI][hapmap]
rs11940320	0.82[EUR][1000 genomes]
rs11946857	0.92[EUR][1000 genomes]
rs12499093	0.82[EUR][1000 genomes]
rs12506592	0.86[TSI][hapmap]
rs12507556	0.83[CEU][hapmap]
rs12508920	0.82[EUR][1000 genomes]
rs12509040	0.80[EUR][1000 genomes]
rs12509066	0.92[EUR][1000 genomes]
rs12510036	0.82[EUR][1000 genomes]
rs1303726	0.82[AFR][1000 genomes]
rs13104293	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13106664	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13113544	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13128286	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13128843	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13132528	0.89[EUR][1000 genomes]
rs13148179	0.90[EUR][1000 genomes]
rs13148603	0.89[EUR][1000 genomes]
rs1379813	0.89[EUR][1000 genomes]
rs1379816	0.89[EUR][1000 genomes]
rs1458236	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1458237	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1458242	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1458243	0.88[EUR][1000 genomes]
rs1458245	0.89[EUR][1000 genomes]
rs1458246	0.89[EUR][1000 genomes]
rs1598904	0.89[EUR][1000 genomes]
rs17605102	0.81[EUR][1000 genomes]
rs1902925	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1902926	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1902927	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1902928	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1962953	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1989329	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1993546	0.82[EUR][1000 genomes]
rs1993547	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2009312	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2017125	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2125305	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2168840	0.92[EUR][1000 genomes]
rs2168841	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2331561	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2331562	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2331577	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3088249	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3749511	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3749513	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3828504	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3966087	0.81[AFR][1000 genomes]
rs4412056	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4518317	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4694358	0.83[EUR][1000 genomes]
rs4694448	0.90[EUR][1000 genomes]
rs4694449	0.90[EUR][1000 genomes]
rs55647928	0.92[EUR][1000 genomes]
rs55795005	0.92[EUR][1000 genomes]
rs6600857	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6843537	0.90[EUR][1000 genomes]
rs6843550	0.92[EUR][1000 genomes]
rs6847539	0.86[EUR][1000 genomes]
rs6849125	0.82[EUR][1000 genomes]
rs6858791	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7435335	0.86[TSI][hapmap]
rs7441753	0.89[EUR][1000 genomes]
rs7666446	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7674475	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7688541	0.81[AFR][1000 genomes]
rs7692753	0.88[EUR][1000 genomes]
rs9329037	0.88[EUR][1000 genomes]
rs969338	0.90[EUR][1000 genomes]
rs994229	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9996467	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9999996	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	esv3398675	chr4:69776413-69778761	Weak transcription Active TSS ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2018150	C4orf7	cis	cerebellum	SCAN
rs2018150	UGT2B7	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69773400-69779200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:69778000-69779000	Enhancers	A549	lung
3	chr4:69778200-69779600	ZNF genes & repeats	Fetal Intestine Large	intestine

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