Variant report

Variant	rs17089132
Chromosome Location	chr4:69047064-69047065
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	RCOR1	chr4:69046833-69047156	Hela-S3	cervix:	n/a	n/a
2	STAT3	chr4:69046612-69047230	MCF10A-Er-Src	breast:	n/a	chr4:69047039-69047047
3	EP300	chr4:69046724-69047277	Hela-S3	cervix:	n/a	n/a
4	STAT3	chr4:69046592-69047230	MCF10A-Er-Src	breast:	n/a	chr4:69047039-69047047
5	TCF7L2	chr4:69046617-69047183	Hela-S3	cervix:	n/a	n/a
6	ZNF143	chr4:69046975-69047085	Hela-S3	cervix:	n/a	n/a
7	EP300	chr4:69046742-69047412	ECC-1	luminal epithelium:	n/a	n/a
8	MYC	chr4:69046815-69047230	MCF10A-Er-Src	breast:	n/a	n/a
9	MYC	chr4:69046958-69047218	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr4:69046570-69047308	MCF10A-Er-Src	breast:	n/a	chr4:69047007-69047016
11	FOS	chr4:69046573-69047258	MCF10A-Er-Src	breast:	n/a	chr4:69047007-69047016
12	FOS	chr4:69046607-69047219	MCF10A-Er-Src	breast:	n/a	chr4:69047007-69047016
13	CEBPB	chr4:69046736-69047277	HCT-116	colon:	n/a	n/a
14	SMC3	chr4:69046740-69047181	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr4:69046473-69047159	MCF10A-Er-Src	breast:	n/a	n/a
16	JUND	chr4:69046571-69047177	Hela-S3	cervix:	n/a	chr4:69047007-69047016
17	TEAD4	chr4:69046785-69047389	ECC-1	luminal epithelium:	n/a	n/a
18	BRCA1	chr4:69046738-69047214	Hela-S3	cervix:	n/a	n/a
19	TEAD4	chr4:69046836-69047311	ECC-1	luminal epithelium:	n/a	n/a
20	STAT3	chr4:69046607-69047230	MCF10A-Er-Src	breast:	n/a	chr4:69047039-69047047
21	FOSL2	chr4:69046793-69047283	A549	lung:	n/a	chr4:69047007-69047016
22	STAT3	chr4:69046872-69047201	Hela-S3	cervix:	n/a	chr4:69047039-69047047
23	STAT3	chr4:69046901-69047515	MCF10A-Er-Src	breast:	n/a	chr4:69047039-69047047
24	FOS	chr4:69046652-69047284	MCF10A-Er-Src	breast:	n/a	chr4:69047007-69047016
25	CHD2	chr4:69046647-69047188	Hela-S3	cervix:	n/a	n/a
26	CEBPB	chr4:69046723-69047292	Hela-S3	cervix:	n/a	n/a
27	EP300	chr4:69046809-69047360	ECC-1	luminal epithelium:	n/a	n/a
28	CEBPB	chr4:69046925-69047238	MCF-7	breast:	n/a	n/a
29	STAT3	chr4:69046666-69047420	MCF10A-Er-Src	breast:	n/a	chr4:69047039-69047047

Variant related genes	Relation type
FTLP10	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10017410	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs10019959	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10023037	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10024312	0.91[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs10030708	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10031769	0.90[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs11934633	0.81[ASN][1000 genomes]
rs11942083	0.90[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11943765	0.90[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs12641295	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12648613	0.90[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs13107652	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs13112221	0.81[ASN][1000 genomes]
rs13115007	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13147086	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13151468	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1370834	0.90[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs28764925	0.81[EUR][1000 genomes]
rs4241685	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4490508	0.86[ASN][1000 genomes]
rs4590097	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4593187	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4860283	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4860902	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62316507	0.80[ASN][1000 genomes]
rs6552148	0.90[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs6819686	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6831923	0.91[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs961736	0.91[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008084	chr4:68797598-69482831	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv537131	chr4:68797598-69482831	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1812438	chr4:68943858-69154222	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv1806586	chr4:68943858-69592846	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv4371	chr4:69046637-69081620	Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69046600-69047200	Enhancers	Monocytes-CD14+_RO01746	blood
2	chr4:69046600-69047400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:69046600-69047400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:69046600-69047400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr4:69046600-69047400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:69046600-69047400	Enhancers	Muscle Satellite Cultured Cells	--
7	chr4:69046600-69047400	Enhancers	HMEC	breast
8	chr4:69046600-69047400	Enhancers	NHEK	skin
9	chr4:69046600-69047800	Enhancers	Hela-S3	cervix
10	chr4:69046800-69047200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr4:69046800-69047400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:69046800-69047400	Enhancers	A549	lung
13	chr4:69046800-69047800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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