Variant report

Variant	rs28890225
Chromosome Location	chr4:69890823-69890824
allele	G/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	RAD21	chr4:69890815-69891334	H1-hESC	embryonic stem cell:	n/a	n/a
2	HNF4A	chr4:69890771-69891228	HepG2	liver:	n/a	chr4:69890920-69890935
3	FOXA1	chr4:69890787-69891375	HepG2	liver:	n/a	n/a
4	CTCF	chr4:69890680-69890830	RPTEC	kidney:	n/a	n/a
5	ARID3A	chr4:69890715-69891247	HepG2	liver:	n/a	n/a
6	FOXA1	chr4:69890728-69891425	HepG2	liver:	n/a	n/a
7	FOXA1	chr4:69890788-69891414	HepG2	liver:	n/a	n/a
8	CTCF	chr4:69890780-69890930	GM12866	blood:	n/a	n/a
9	EP300	chr4:69890736-69891332	HepG2	liver:	n/a	n/a
10	FOXA2	chr4:69890736-69891351	HepG2	liver:	n/a	n/a
11	FOXA1	chr4:69890793-69891379	HepG2	liver:	n/a	n/a
12	RAD21	chr4:69890793-69891443	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000250919	TF binding region
ENSG00000249890	TF binding region
ENSG00000251685	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10008743	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10009634	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10014355	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10030409	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10050146	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10213292	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28375844	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28410179	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28454605	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28458345	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28462361	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28472596	1.00[EUR][1000 genomes]
rs28535667	1.00[EUR][1000 genomes]
rs28539948	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28578474	0.96[EUR][1000 genomes]
rs28637446	1.00[EUR][1000 genomes]
rs28675300	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28678018	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28678791	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28684869	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28685210	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28726088	0.84[EUR][1000 genomes]
rs28754965	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28821804	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34661811	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4299663	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4412057	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56028004	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57913007	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59592861	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60930838	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72855405	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73823805	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73823851	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73823857	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73823859	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73823860	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73826062	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9985807	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9993579	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9995928	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9999964	0.96[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	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
2	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
3	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
4	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
5	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
6	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
7	nsv594582	chr4:69827340-69988378	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	esv2757064	chr4:69863174-69901607	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv980213	chr4:69870183-69893292	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv879379	chr4:69878929-69987249	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69886000-69891000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr4:69886200-69893000	Enhancers	HepG2	liver
3	chr4:69887400-69891200	Weak transcription	A549	lung
4	chr4:69889800-69891400	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr4:69889800-69891400	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr4:69889800-69891400	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr4:69890000-69891000	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr4:69890000-69891400	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr4:69890800-69891000	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr4:69890800-69891200	Enhancers	H1 Cell Line	embryonic stem cell
11	chr4:69890800-69891200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:69890800-69891200	Enhancers	Liver	Liver
13	chr4:69890800-69891200	Enhancers	Fetal Intestine Large	intestine
14	chr4:69890800-69891600	Enhancers	Stomach Mucosa	stomach

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