Variant report

Variant	rs4700353
Chromosome Location	chr5:59322139-59322140
allele	A/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	FOS	chr5:59322110-59322247	MCF10A-Er-Src	breast:	n/a	chr5:59322142-59322152 chr5:59322143-59322151 chr5:59322143-59322150 chr5:59322143-59322151 chr5:59322141-59322153
2	TCF12	chr5:59321832-59322572	SK-N-SH	brain:	n/a	n/a
3	FOSL2	chr5:59321903-59322505	SK-N-SH	brain:	n/a	chr5:59322142-59322152 chr5:59322143-59322151 chr5:59322143-59322150 chr5:59322143-59322151 chr5:59322141-59322153
4	EP300	chr5:59321863-59322568	SK-N-SH	brain:	n/a	chr5:59322143-59322152
5	TCF12	chr5:59321837-59322593	SK-N-SH	brain:	n/a	n/a
6	FOS	chr5:59322111-59322233	MCF10A-Er-Src	breast:	n/a	chr5:59322142-59322152 chr5:59322143-59322151 chr5:59322143-59322150 chr5:59322143-59322151 chr5:59322141-59322153
7	FOS	chr5:59321932-59322210	MCF10A-Er-Src	breast:	n/a	chr5:59322142-59322152 chr5:59322143-59322151 chr5:59322143-59322150 chr5:59322143-59322151 chr5:59322141-59322153
8	EP300	chr5:59321956-59322351	Hela-S3	cervix:	n/a	chr5:59322143-59322152
9	JUND	chr5:59321818-59322535	SK-N-SH	brain:	n/a	chr5:59322142-59322152 chr5:59322143-59322151 chr5:59322143-59322150 chr5:59322143-59322151 chr5:59322141-59322153
10	FOS	chr5:59322064-59322265	MCF10A-Er-Src	breast:	n/a	chr5:59322142-59322152 chr5:59322143-59322151 chr5:59322143-59322150 chr5:59322143-59322151 chr5:59322141-59322153
11	PBX3	chr5:59321949-59322502	SK-N-SH	brain:	n/a	n/a
12	GATA3	chr5:59321844-59322607	SK-N-SH	brain:	n/a	chr5:59322226-59322236 chr5:59322466-59322476 chr5:59322229-59322236
13	NFIC	chr5:59321922-59322495	SK-N-SH	brain:	n/a	n/a
14	GATA3	chr5:59321799-59322650	SK-N-SH	brain:	n/a	chr5:59322226-59322236 chr5:59322466-59322476 chr5:59322229-59322236
15	PBX3	chr5:59321900-59322503	SK-N-SH	brain:	n/a	n/a
16	CEBPB	chr5:59321960-59322375	Hela-S3	cervix:	n/a	n/a
17	EP300	chr5:59322049-59322335	SK-N-SH_RA	brain:	n/a	chr5:59322143-59322152
18	NFIC	chr5:59321908-59322406	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000248935	TF binding region

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10041046	0.91[CEU][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10041093	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10044734	0.84[EUR][1000 genomes]
rs10045507	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10066957	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10068194	0.82[JPT][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10070511	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10223314	0.85[EUR][1000 genomes]
rs10223317	0.96[CEU][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes]
rs10461667	0.82[CHB][hapmap]
rs10805519	1.00[CEU][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10939837	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs10940659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1100918	0.84[CHB][hapmap]
rs1155796	0.84[CHB][hapmap]
rs11949645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12187454	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12515390	1.00[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs12522531	1.00[CEU][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs12656920	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12657321	0.85[EUR][1000 genomes]
rs13154041	0.84[CHB][hapmap]
rs13157868	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13162028	1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13162265	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13164245	0.84[CHB][hapmap]
rs13164971	0.84[CHB][hapmap]
rs13168606	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs13179619	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs13184535	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13189802	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs1396474	0.81[JPT][hapmap]
rs1508862	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1508864	0.84[CHB][hapmap]
rs1533020	1.00[CEU][hapmap]
rs1544790	0.84[CHB][hapmap]
rs1588265	0.84[CHB][hapmap]
rs1848499	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1969156	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs1981848	1.00[CEU][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs1995780	1.00[CEU][hapmap];0.87[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2016324	0.84[CHB][hapmap]
rs2089577	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2113076	0.85[EUR][1000 genomes]
rs2136202	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2194255	1.00[CEU][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes]
rs2216726	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs2548658	0.89[CHB][hapmap]
rs2548659	0.84[CHB][hapmap]
rs2662444	0.89[CHB][hapmap]
rs2962962	0.84[CHB][hapmap]
rs2962966	0.88[CHB][hapmap]
rs2962975	0.84[CHB][hapmap]
rs4538573	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs4547891	0.84[CHB][hapmap]
rs4569833	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs4699951	0.83[EUR][1000 genomes]
rs4699952	0.95[CEU][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs4700354	0.84[CHB][hapmap]
rs4700355	0.84[CHB][hapmap]
rs4700359	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4700365	1.00[CEU][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs58883323	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62370616	0.84[EUR][1000 genomes]
rs6449456	0.84[CHB][hapmap]
rs6449458	0.84[EUR][1000 genomes]
rs6859376	1.00[CEU][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs6872268	0.84[CHB][hapmap]
rs6881029	0.86[EUR][1000 genomes]
rs7444851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7703240	1.00[CEU][hapmap];0.87[JPT][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7703245	0.84[CHB][hapmap]
rs7714067	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs7715725	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs7719879	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs7731007	0.84[CHB][hapmap]
rs7732249	0.81[JPT][hapmap]
rs7733728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7734168	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs851280	1.00[CEU][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes]
rs851281	0.86[EUR][1000 genomes]
rs851282	0.85[EUR][1000 genomes]
rs860374	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs864064	0.85[EUR][1000 genomes]
rs865892	0.85[EUR][1000 genomes]
rs983279	1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs996234	0.96[CEU][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv534614	chr5:58962510-59388525	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv1027171	chr5:59267959-59340525	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv881709	chr5:59307813-59437874	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv881710	chr5:59311463-59437874	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59316400-59322400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr5:59317600-59330000	Weak transcription	Aorta	Aorta
3	chr5:59320800-59329600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:59321800-59322600	Enhancers	A549	lung
5	chr5:59321800-59322600	Enhancers	Hela-S3	cervix
6	chr5:59322000-59322400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:59322000-59322600	Enhancers	Muscle Satellite Cultured Cells	--
8	chr5:59322000-59322600	Enhancers	NH-A	brain

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