Variant report

Variant	rs13201590
Chromosome Location	chr6:4603912-4603913
allele	C/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	SPI1	chr6:4603610-4604016	HL-60	blood:	n/a	n/a
2	STAT3	chr6:4603314-4604142	MCF10A-Er-Src	breast:	n/a	chr6:4603705-4603714 chr6:4603704-4603713
3	FOS	chr6:4603444-4604019	MCF10A-Er-Src	breast:	n/a	chr6:4603701-4603712 chr6:4603704-4603713 chr6:4603705-4603713 chr6:4603706-4603713
4	STAT3	chr6:4603422-4604124	MCF10A-Er-Src	breast:	n/a	chr6:4603705-4603714 chr6:4603704-4603713
5	FOS	chr6:4603374-4604128	MCF10A-Er-Src	breast:	n/a	chr6:4603701-4603712 chr6:4603704-4603713 chr6:4603705-4603713 chr6:4603706-4603713
6	STAT3	chr6:4603404-4604129	MCF10A-Er-Src	breast:	n/a	chr6:4603705-4603714 chr6:4603704-4603713
7	STAT3	chr6:4603520-4603974	MCF10A-Er-Src	breast:	n/a	chr6:4603705-4603714 chr6:4603704-4603713
8	MYC	chr6:4603366-4604010	MCF10A-Er-Src	breast:	n/a	chr6:4603705-4603714 chr6:4603433-4603442
9	POLR2A	chr6:4603517-4604225	MCF10A-Er-Src	breast:	n/a	n/a
10	E2F4	chr6:4603495-4603951	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr6:4603313-4604122	MCF10A-Er-Src	breast:	n/a	chr6:4603701-4603712 chr6:4603704-4603713 chr6:4603705-4603713 chr6:4603706-4603713
12	MYC	chr6:4603294-4604032	MCF10A-Er-Src	breast:	n/a	chr6:4603705-4603714 chr6:4603433-4603442
13	FOS	chr6:4603466-4604006	MCF10A-Er-Src	breast:	n/a	chr6:4603701-4603712 chr6:4603704-4603713 chr6:4603705-4603713 chr6:4603706-4603713

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4585158..4587342-chr6:4603749..4606503,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260673	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2235725	0.85[EUR][1000 genomes]
rs2326529	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2875952	0.90[EUR][1000 genomes]
rs34795311	0.83[EUR][1000 genomes]
rs35306133	0.81[EUR][1000 genomes]
rs3748077	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs3812185	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6597082	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6920804	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71547273	0.81[EUR][1000 genomes]
rs7771456	0.83[EUR][1000 genomes]
rs7772288	0.85[EUR][1000 genomes]
rs9791204	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3421990	chr6:4446933-4659639	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv830576	chr6:4447554-4610604	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv3366530	chr6:4471528-4865322	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv883415	chr6:4546491-4629654	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4599800-4604000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:4599800-4604400	Enhancers	NHEK	skin
3	chr6:4600000-4604400	Enhancers	HMEC	breast
4	chr6:4600000-4606800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr6:4600400-4604400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:4601000-4607000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:4601200-4606400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:4601200-4606400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr6:4601200-4606400	Weak transcription	Right Ventricle	heart
10	chr6:4601400-4607000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:4601600-4606000	Weak transcription	Fetal Muscle Leg	muscle
12	chr6:4601600-4606800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr6:4601800-4604000	Enhancers	Placenta Amnion	Placenta Amnion
14	chr6:4601800-4607000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:4602400-4604400	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr6:4602400-4604400	Enhancers	Placenta	Placenta
17	chr6:4602600-4606400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:4602800-4604400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:4603000-4604000	Enhancers	HSMMtube	muscle
20	chr6:4603000-4604000	Enhancers	NHLF	lung
21	chr6:4603000-4604200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:4603000-4604400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:4603000-4604400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:4603000-4604400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:4603000-4604400	Enhancers	NH-A	brain
26	chr6:4603000-4604600	Enhancers	HSMM	muscle
27	chr6:4603200-4604000	Enhancers	Muscle Satellite Cultured Cells	--
28	chr6:4603200-4604000	Enhancers	K562	blood
29	chr6:4603200-4604400	Enhancers	Fetal Heart	heart
30	chr6:4603200-4604400	Enhancers	NHDF-Ad	bronchial
31	chr6:4603200-4604400	Enhancers	Osteobl	bone
32	chr6:4603400-4608800	Weak transcription	Spleen	Spleen
33	chr6:4603600-4606400	Weak transcription	Adipose Nuclei	Adipose
34	chr6:4603600-4606800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr6:4603600-4607200	Weak transcription	Esophagus	oesophagus
36	chr6:4603800-4604000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:4603800-4604000	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr6:4603800-4604200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:4603800-4604400	Enhancers	HUVEC	blood vessel
40	chr6:4603800-4606400	Weak transcription	Lung	lung

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