Variant report

Variant	rs2007513
Chromosome Location	chr6:4608253-4608254
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	NFIC	chr6:4606917-4608334	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr6:4607057-4608299	ECC-1	luminal epithelium:	n/a	n/a
3	MXI1	chr6:4608238-4608429	GM12878	blood:	n/a	n/a
4	FOXM1	chr6:4607030-4608354	ECC-1	luminal epithelium:	n/a	n/a
5	TCF12	chr6:4607206-4608366	ECC-1	luminal epithelium:	n/a	chr6:4607848-4607855

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	chr6:4608105..4609645-chr6:4609883..4611653,2	MCF-7	breast:

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

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs6597081	0.94[TSI][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2007513	FOXC1	cis	cerebellum	SCAN
rs2007513	RIOK1	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4603400-4608800	Weak transcription	Spleen	Spleen
2	chr6:4604400-4610200	Weak transcription	Fetal Heart	heart
3	chr6:4606000-4616800	Enhancers	Fetal Muscle Leg	muscle
4	chr6:4606400-4609000	Enhancers	Adipose Nuclei	Adipose
5	chr6:4606400-4609200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:4606400-4610600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:4606400-4612200	Enhancers	Placenta	Placenta
8	chr6:4606800-4609000	Enhancers	HUVEC	blood vessel
9	chr6:4606800-4609400	Enhancers	Brain Germinal Matrix	brain
10	chr6:4606800-4610600	Weak transcription	Left Ventricle	heart
11	chr6:4607000-4608400	Enhancers	Ovary	ovary
12	chr6:4607000-4608600	Flanking Active TSS	Brain Hippocampus Middle	brain
13	chr6:4607000-4609000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr6:4607000-4610400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:4607200-4608400	Enhancers	Fetal Kidney	kidney
16	chr6:4607200-4609400	Enhancers	NHLF	lung
17	chr6:4607400-4608400	Enhancers	Hela-S3	cervix
18	chr6:4607400-4608400	Bivalent Enhancer	K562	blood
19	chr6:4607400-4611800	Weak transcription	Colon Smooth Muscle	Colon
20	chr6:4607600-4608400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr6:4607600-4608400	Enhancers	HMEC	breast
22	chr6:4607600-4608400	Enhancers	NH-A	brain
23	chr6:4607600-4608800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:4607600-4608800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr6:4607600-4608800	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr6:4607600-4608800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr6:4607600-4608800	Weak transcription	Right Atrium	heart
28	chr6:4607600-4608800	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr6:4607600-4609200	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr6:4607600-4609400	Enhancers	HSMM	muscle
31	chr6:4607600-4610400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr6:4607600-4610600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr6:4607600-4610800	Weak transcription	Right Ventricle	heart
34	chr6:4607600-4611000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr6:4607600-4613200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:4607600-4615200	Weak transcription	Lung	lung
37	chr6:4608000-4608400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:4608000-4608400	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr6:4608000-4608400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:4608000-4608400	Enhancers	Brain Substantia Nigra	brain
41	chr6:4608000-4608400	Enhancers	Stomach Smooth Muscle	stomach
42	chr6:4608000-4608800	Enhancers	Muscle Satellite Cultured Cells	--
43	chr6:4608000-4608800	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr6:4608000-4609000	Enhancers	Primary hematopoietic stem cells	blood
45	chr6:4608000-4609400	Enhancers	HSMMtube	muscle
46	chr6:4608000-4610800	Weak transcription	Aorta	Aorta
47	chr6:4608000-4611000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr6:4608000-4611200	Weak transcription	Fetal Brain Male	brain
49	chr6:4608000-4611800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr6:4608200-4608400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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