Variant report

Variant	rs9502208
Chromosome Location	chr6:4607325-4607326
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	FOS	chr6:4607256-4607354	MCF10A-Er-Src	breast:	n/a	n/a
2	NFIC	chr6:4606917-4608334	ECC-1	luminal epithelium:	n/a	n/a
3	TEAD4	chr6:4607179-4608195	ECC-1	luminal epithelium:	n/a	n/a
4	SP1	chr6:4607080-4608166	HCT-116	colon:	n/a	chr6:4607967-4607988
5	NFIC	chr6:4607057-4608299	ECC-1	luminal epithelium:	n/a	n/a
6	EP300	chr6:4607239-4608171	ECC-1	luminal epithelium:	n/a	chr6:4607790-4607799
7	TEAD4	chr6:4607147-4608142	ECC-1	luminal epithelium:	n/a	n/a
8	TCF12	chr6:4607292-4608026	SK-N-SH	brain:	n/a	chr6:4607848-4607855
9	FOSL1	chr6:4607258-4608164	HCT-116	colon:	n/a	chr6:4607669-4607676 chr6:4607792-4607799 chr6:4607659-4607667 chr6:4607790-4607799
10	TCF7L2	chr6:4607053-4607913	PANC-1	pancreas:	n/a	n/a
11	TCF7L2	chr6:4607075-4607909	MCF-7	breast:	n/a	n/a
12	SIN3AK20	chr6:4607150-4608169	MCF-7	breast:	n/a	n/a
13	TCF12	chr6:4607151-4608217	ECC-1	luminal epithelium:	n/a	chr6:4607848-4607855
14	RAD21	chr6:4607217-4608097	ECC-1	luminal epithelium:	n/a	n/a
15	TCF12	chr6:4607270-4607997	SK-N-SH	brain:	n/a	chr6:4607848-4607855
16	FOXM1	chr6:4607030-4608354	ECC-1	luminal epithelium:	n/a	n/a
17	NFIC	chr6:4607183-4608147	SK-N-SH	brain:	n/a	n/a
18	MAX	chr6:4607166-4608026	MCF-7	breast:	n/a	chr6:4607556-4607565
19	FOS	chr6:4607287-4607359	MCF10A-Er-Src	breast:	n/a	n/a
20	FOSL1	chr6:4607149-4608183	HCT-116	colon:	n/a	chr6:4607669-4607676 chr6:4607792-4607799 chr6:4607659-4607667 chr6:4607790-4607799
21	TCF12	chr6:4607206-4608366	ECC-1	luminal epithelium:	n/a	chr6:4607848-4607855
22	JUND	chr6:4607193-4608180	HCT-116	colon:	n/a	chr6:4607669-4607676 chr6:4607792-4607799 chr6:4607659-4607667 chr6:4607790-4607799
23	MAX	chr6:4607089-4608045	ECC-1	luminal epithelium:	n/a	chr6:4607556-4607565
24	FOXM1	chr6:4607264-4608174	ECC-1	luminal epithelium:	n/a	n/a
25	HDAC2	chr6:4607164-4607991	MCF-7	breast:	n/a	n/a
26	SP1	chr6:4607105-4608178	HCT-116	colon:	n/a	chr6:4607967-4607988
27	STAT3	chr6:4607197-4607351	MCF10A-Er-Src	breast:	n/a	n/a
28	ESR1	chr6:4607249-4608086	ECC-1	luminal epithelium:	n/a	n/a
29	EP300	chr6:4607031-4608244	ECC-1	luminal epithelium:	n/a	chr6:4607790-4607799 chr6:4607179-4607193
30	MAX	chr6:4607089-4608038	ECC-1	luminal epithelium:	n/a	chr6:4607556-4607565

No.	Distal block	Cell Line	Cell type
1	chr6:4606187..4608803-chr6:4609320..4611011,2	K562	blood:
2	chr6:4606412..4609387-chr6:4772936..4775041,2	MCF-7	breast:
3	chr6:4601505..4603151-chr6:4605939..4607714,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260673	TF binding region
ENSG00000205444	TF binding region
ENSG00000153046	Chromatin interaction
ENSG00000205444	Chromatin interaction
ENSG00000260673	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11964427	1.00[ASN][1000 genomes]
rs2143455	0.81[EUR][1000 genomes]
rs4960005	0.82[EUR][1000 genomes]
rs4960006	0.82[EUR][1000 genomes]
rs6911463	1.00[GIH][hapmap]
rs6912325	1.00[ASN][1000 genomes]
rs7764724	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9502204	0.82[EUR][1000 genomes]
rs9502205	0.82[EUR][1000 genomes]
rs9504160	0.82[EUR][1000 genomes]
rs9504165	0.90[GIH][hapmap]
rs9504168	0.89[ASN][1000 genomes]
rs9504169	0.89[ASN][1000 genomes]

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	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
5	nsv970370	chr6:4605843-4619763	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4603400-4608800	Weak transcription	Spleen	Spleen
2	chr6:4604400-4607800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:4604400-4610200	Weak transcription	Fetal Heart	heart
4	chr6:4605400-4607600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:4606000-4616800	Enhancers	Fetal Muscle Leg	muscle
6	chr6:4606400-4607600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:4606400-4607600	Enhancers	Lung	lung
8	chr6:4606400-4607600	Enhancers	Right Ventricle	heart
9	chr6:4606400-4608000	Enhancers	Primary T cells fromperipheralblood	blood
10	chr6:4606400-4608200	Enhancers	Fetal Stomach	stomach
11	chr6:4606400-4609000	Enhancers	Adipose Nuclei	Adipose
12	chr6:4606400-4609200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:4606400-4610600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr6:4606400-4612200	Enhancers	Placenta	Placenta
15	chr6:4606600-4608000	Enhancers	Fetal Brain Male	brain
16	chr6:4606600-4608200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:4606800-4607600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:4606800-4608200	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr6:4606800-4609000	Enhancers	HUVEC	blood vessel
20	chr6:4606800-4609400	Enhancers	Brain Germinal Matrix	brain
21	chr6:4606800-4610600	Weak transcription	Left Ventricle	heart
22	chr6:4607000-4607400	Flanking Active TSS	Brain Angular Gyrus	brain
23	chr6:4607000-4607400	Flanking Active TSS	Brain Substantia Nigra	brain
24	chr6:4607000-4607400	Enhancers	Colon Smooth Muscle	Colon
25	chr6:4607000-4607600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:4607000-4607600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr6:4607000-4607600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr6:4607000-4607600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr6:4607000-4607600	Flanking Active TSS	Brain Anterior Caudate	brain
30	chr6:4607000-4607600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
31	chr6:4607000-4607600	Enhancers	Fetal Brain Female	brain
32	chr6:4607000-4607600	Enhancers	Pancreas	Pancrea
33	chr6:4607000-4607600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
34	chr6:4607000-4607600	Enhancers	Rectal Smooth Muscle	rectum
35	chr6:4607000-4607600	Enhancers	Right Atrium	heart
36	chr6:4607000-4607600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr6:4607000-4607600	Flanking Active TSS	Stomach Smooth Muscle	stomach
38	chr6:4607000-4607600	Flanking Active TSS	HMEC	breast
39	chr6:4607000-4607600	Flanking Active TSS	HSMM	muscle
40	chr6:4607000-4608000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:4607000-4608000	Flanking Active TSS	Brain Cingulate Gyrus	brain
42	chr6:4607000-4608000	Flanking Active TSS	HSMMtube	muscle
43	chr6:4607000-4608000	Enhancers	NHEK	skin
44	chr6:4607000-4608200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr6:4607000-4608200	Enhancers	Psoas Muscle	Psoas
46	chr6:4607000-4608200	Flanking Active TSS	Osteobl	bone
47	chr6:4607000-4608400	Enhancers	Ovary	ovary
48	chr6:4607000-4608600	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr6:4607000-4609000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr6:4607000-4610400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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