Variant report

Variant	rs6533372
Chromosome Location	chr4:78911389-78911390
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	USF1	chr4:78911117-78911604	HCT-116	colon:	n/a	chr4:78911329-78911340
2	USF1	chr4:78911172-78911438	SK-N-SH_RA	brain:	n/a	chr4:78911329-78911340
3	USF1	chr4:78911149-78911505	ECC-1	luminal epithelium:	n/a	chr4:78911329-78911340
4	USF1	chr4:78911173-78911550	ECC-1	luminal epithelium:	n/a	chr4:78911329-78911340
5	USF1	chr4:78911180-78911520	SK-N-SH	brain:	n/a	chr4:78911329-78911340
6	USF1	chr4:78911226-78911441	HepG2	liver:	n/a	chr4:78911329-78911340
7	USF2	chr4:78911217-78911486	HepG2	liver:	n/a	n/a
8	NFYB	chr4:78911128-78911491	GM12878	blood:	n/a	n/a
9	USF1	chr4:78911139-78911489	SK-N-SH_RA	brain:	n/a	chr4:78911329-78911340
10	USF1	chr4:78911199-78911436	HepG2	liver:	n/a	chr4:78911329-78911340
11	USF1	chr4:78911095-78911509	H1-hESC	embryonic stem cell:	n/a	chr4:78911329-78911340
12	NFYB	chr4:78911111-78911491	K562	blood:	n/a	n/a
13	USF2	chr4:78911276-78911418	GM12878	blood:	n/a	n/a
14	USF1	chr4:78911143-78911467	K562	blood:	n/a	chr4:78911329-78911340
15	MAX	chr4:78911304-78911436	HepG2	liver:	n/a	n/a
16	USF1	chr4:78911129-78911463	H1-hESC	embryonic stem cell:	n/a	chr4:78911329-78911340
17	USF1	chr4:78911187-78911476	K562	blood:	n/a	chr4:78911329-78911340
18	EP300	chr4:78911101-78914215	SK-N-SH	brain:	n/a	chr4:78913240-78913249 chr4:78911637-78911646 chr4:78912160-78912174

Variant related genes	Relation type
HNRNPA1P56	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10005531	0.84[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs10019920	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.88[ASN][1000 genomes]
rs10026176	0.80[CEU][hapmap];0.89[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs10027739	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10030568	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.93[ASN][1000 genomes]
rs10049674	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.85[ASN][1000 genomes]
rs1106457	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11931471	0.94[ASN][1000 genomes]
rs11931686	0.80[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs12509847	0.80[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs13131974	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1393643	0.93[ASN][1000 genomes]
rs1604609	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2036455	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs2036457	0.84[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs2088995	0.93[ASN][1000 genomes]
rs2102192	0.96[ASN][1000 genomes]
rs28417234	0.91[ASN][1000 genomes]
rs28483318	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4128860	0.84[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs4859512	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.85[ASN][1000 genomes]
rs4859513	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4859882	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs4859884	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs4859890	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6533355	0.88[ASN][1000 genomes]
rs6814088	0.88[ASN][1000 genomes]
rs6820725	0.90[ASN][1000 genomes]
rs6849145	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs7436080	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.93[ASN][1000 genomes]
rs7682450	0.80[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs873280	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs924684	0.84[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs924685	0.84[CEU][hapmap];0.86[ASN][1000 genomes]
rs9654194	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs9985806	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752050	chr4:78693311-78975321	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1010714	chr4:78742505-78991030	Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv516836	chr4:78748977-78981919	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv594704	chr4:78748977-78981919	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv461562	chr4:78757015-78981919	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv461563	chr4:78757015-78981919	Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv594705	chr4:78757015-78981919	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1008217	chr4:78777531-78957311	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv537145	chr4:78777531-78957311	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
11	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
12	nsv1004772	chr4:78906866-78976561	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78911000-78913800	Enhancers	Fetal Lung	lung
2	chr4:78911200-78911400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr4:78911200-78912200	Enhancers	Fetal Stomach	stomach
4	chr4:78911200-78912600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:78911200-78912600	Enhancers	Fetal Brain Male	brain
6	chr4:78911200-78912600	Enhancers	HepG2	liver

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