Variant report

Variant	rs4859477
Chromosome Location	chr4:78142698-78142699
allele	A/G
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	FOS	chr4:78142471-78142856	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr4:78142544-78142707	MCF10A-Er-Src	breast:	n/a	n/a
3	CEBPB	chr4:78142464-78142815	Hela-S3	cervix:	n/a	n/a
4	MAX	chr4:78142595-78142795	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr4:78142460-78142826	IMR90	lung:	n/a	n/a
6	MYC	chr4:78142496-78142928	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr4:78142492-78142940	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr4:78142607-78142777	MCF10A-Er-Src	breast:	n/a	n/a
9	USF2	chr4:78142519-78142866	Hela-S3	cervix:	n/a	n/a
10	MYC	chr4:78142389-78142872	MCF10A-Er-Src	breast:	n/a	n/a
11	USF1	chr4:78142560-78142779	K562	blood:	n/a	n/a
12	FOS	chr4:78142480-78142929	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr4:78142467-78142913	MCF10A-Er-Src	breast:	n/a	n/a
14	STAT3	chr4:78142589-78142814	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000270669	TF binding region

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10005142	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10009384	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10010290	0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10018359	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10020351	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10025838	0.90[JPT][hapmap]
rs10026129	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10026795	0.84[ASN][1000 genomes]
rs10030727	0.80[ASN][1000 genomes]
rs10030735	0.96[CEU][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs10030867	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs10030957	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1006042	0.90[JPT][hapmap]
rs10856957	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11097729	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11097730	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11097741	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12504397	0.82[ASN][1000 genomes]
rs12508219	0.83[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12509168	0.91[JPT][hapmap]
rs12640093	0.90[JPT][hapmap]
rs1477314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1559119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1559122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1968235	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2042228	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28503908	0.81[CEU][hapmap]
rs4280759	0.91[JPT][hapmap]
rs4285107	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4504280	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4536958	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4538513	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4547817	0.90[JPT][hapmap]
rs4563522	0.89[JPT][hapmap]
rs4576030	0.93[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4582179	0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4582180	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4859475	0.92[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4859752	0.93[CEU][hapmap]
rs4859753	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4859754	0.93[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4859755	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4859756	0.90[JPT][hapmap]
rs4859758	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6532904	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6532919	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6532921	0.92[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6822794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6838744	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6840915	0.96[CEU][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6844009	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6845599	0.96[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6846698	0.91[JPT][hapmap]
rs6857792	0.93[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs7690427	0.88[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000730	chr4:78109138-78210296	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1011551	chr4:78120872-78204224	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1012298	chr4:78120872-78255427	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv997743	chr4:78126462-78217004	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1014055	chr4:78132200-78255427	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1013602	chr4:78133566-78217004	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1007726	chr4:78133566-78255427	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1001852	chr4:78135874-78260269	ZNF genes & repeats Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1013302	chr4:78136251-78192318	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv998972	chr4:78139780-78240303	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1010406	chr4:78139780-78255427	Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1014305	chr4:78139780-78260269	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv1006017	chr4:78139780-78312974	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78125200-78143600	Weak transcription	Primary B cells from cord blood	blood
2	chr4:78140200-78144000	Enhancers	Fetal Heart	heart
3	chr4:78141800-78142800	Enhancers	Fetal Muscle Leg	muscle
4	chr4:78141800-78143200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:78142000-78143000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:78142000-78143000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:78142200-78142800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:78142200-78142800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr4:78142200-78143200	Bivalent Enhancer	Osteobl	bone
10	chr4:78142600-78143200	Enhancers	Fetal Lung	lung

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