Variant report

Variant	rs6677468
Chromosome Location	chr1:179555365-179555366
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	MAFK	chr1:179555265-179555464	HepG2	liver:	n/a	chr1:179555339-179555353
2	MAX	chr1:179555176-179555982	MCF-7	breast:	n/a	n/a
3	CREB1	chr1:179555338-179555838	A549	lung:	n/a	n/a
4	CTCF	chr1:179555350-179555820	K562	blood:	n/a	chr1:179555549-179555562
5	CTCF	chr1:179555353-179555799	T-47D	breast:	n/a	chr1:179555549-179555562
6	NR3C1	chr1:179555122-179555611	ECC-1	luminal epithelium:	n/a	chr1:179555288-179555304 chr1:179555289-179555303 chr1:179555285-179555306 chr1:179555289-179555303 chr1:179555288-179555304 chr1:179555287-179555305 chr1:179555287-179555304 chr1:179555283-179555309 chr1:179555288-179555304 chr1:179555288-179555304
7	HA-E2F1	chr1:179555139-179556249	MCF-7	breast:	n/a	chr1:179555739-179555746 chr1:179555147-179555156
8	MAFK	chr1:179555176-179555499	IMR90	lung:	n/a	chr1:179555339-179555353
9	ATF2	chr1:179555091-179555606	H1-hESC	embryonic stem cell:	n/a	n/a
10	EGR1	chr1:179555360-179555966	H1-hESC	embryonic stem cell:	n/a	chr1:179555414-179555427
11	RAD21	chr1:179555357-179555810	H1-hESC	embryonic stem cell:	n/a	n/a
12	TBP	chr1:179555330-179556014	H1-hESC	embryonic stem cell:	n/a	n/a
13	HDAC2	chr1:179555255-179556159	MCF-7	breast:	n/a	n/a
14	UBTF	chr1:179555347-179555717	K562	blood:	n/a	n/a
15	MAFK	chr1:179555156-179555458	H1-hESC	embryonic stem cell:	n/a	chr1:179555339-179555353
16	E2F6	chr1:179555339-179555845	A549	lung:	n/a	chr1:179555739-179555746
17	ATF2	chr1:179555115-179555687	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr1:179555013-179556347	SK-N-SH	brain:	n/a	chr1:179555549-179555562
19	JUN	chr1:179555155-179555436	H1-hESC	embryonic stem cell:	n/a	n/a
20	ZNF384	chr1:179555180-179555717	K562	blood:	n/a	n/a
21	MAX	chr1:179555325-179556051	ECC-1	luminal epithelium:	n/a	n/a
22	CTCF	chr1:179555243-179555963	MCF-7	breast:	n/a	chr1:179555549-179555562
23	NR3C1	chr1:179555142-179555411	ECC-1	luminal epithelium:	n/a	chr1:179555288-179555304 chr1:179555289-179555303 chr1:179555285-179555306 chr1:179555289-179555303 chr1:179555288-179555304 chr1:179555287-179555305 chr1:179555287-179555304 chr1:179555283-179555309 chr1:179555288-179555304 chr1:179555288-179555304
24	FOXA2	chr1:179555342-179555981	A549	lung:	n/a	n/a
25	MAX	chr1:179555322-179555859	H1-hESC	embryonic stem cell:	n/a	n/a
26	ZBTB7A	chr1:179555319-179555784	ECC-1	luminal epithelium:	n/a	n/a
27	HMGN3	chr1:179555340-179555767	K562	blood:	n/a	n/a
28	MAX	chr1:179555289-179555876	A549	lung:	n/a	n/a
29	MAX	chr1:179555275-179555937	A549	lung:	n/a	n/a
30	CTCF	chr1:179555349-179555925	K562	blood:	n/a	chr1:179555549-179555562
31	CTCF	chr1:179555346-179555763	K562	blood:	n/a	chr1:179555549-179555562
32	CTCF	chr1:179555359-179555766	H1-hESC	embryonic stem cell:	n/a	chr1:179555549-179555562
33	E2F4	chr1:179555339-179555539	MCF10A-Er-Src	breast:	n/a	n/a
34	TAF1	chr1:179555318-179555622	H1-hESC	embryonic stem cell:	n/a	n/a
35	JUND	chr1:179555158-179555710	H1-hESC	embryonic stem cell:	n/a	n/a
36	YY1	chr1:179555355-179555745	SK-N-SH_RA	brain:	n/a	chr1:179555675-179555686
37	CTCF	chr1:179555360-179555510	HVMF	connective:	n/a	n/a
38	RAD21	chr1:179555236-179555840	H1-hESC	embryonic stem cell:	n/a	n/a
39	RAD21	chr1:179555331-179555786	SK-N-SH_RA	brain:	n/a	n/a
40	CCNT2	chr1:179555350-179555735	K562	blood:	n/a	n/a
41	CTCF	chr1:179554976-179556053	A549	lung:	n/a	chr1:179555549-179555562
42	TCF12	chr1:179555321-179555976	ECC-1	luminal epithelium:	n/a	n/a
43	MAFK	chr1:179555223-179555457	HepG2	liver:	n/a	chr1:179555339-179555353
44	E2F6	chr1:179555220-179555775	H1-hESC	embryonic stem cell:	n/a	chr1:179555739-179555746
45	THAP1	chr1:179555319-179555532	K562	blood:	n/a	n/a
46	NANOG	chr1:179555350-179555718	H1-hESC	embryonic stem cell:	n/a	n/a
47	YY1	chr1:179555347-179555682	ECC-1	luminal epithelium:	n/a	n/a
48	TAF1	chr1:179555300-179555617	ECC-1	luminal epithelium:	n/a	n/a
49	TAF1	chr1:179555317-179555635	H1-hESC	embryonic stem cell:	n/a	n/a
50	CREB1	chr1:179555364-179555700	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:179555238..179555794-chr1:179568470..179568984,2	MCF-7	breast:
2	chr1:179543048..179545135-chr1:179554204..179557043,2	K562	blood:
3	chr1:179553040..179558877-chr1:179559940..179564416,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227141	TF binding region
ENSG00000261060	TF binding region
ENSG00000116218	Chromatin interaction
ENSG00000162782	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10798697	0.83[ASN][1000 genomes]
rs10913830	0.83[ASN][1000 genomes]
rs11805051	0.83[ASN][1000 genomes]
rs12121642	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12565489	0.83[ASN][1000 genomes]
rs6677476	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72706715	0.83[ASN][1000 genomes]
rs72706717	0.83[ASN][1000 genomes]
rs7549026	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179553600-179555400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:179554600-179555400	Enhancers	Fetal Kidney	kidney
3	chr1:179555000-179555400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
4	chr1:179555000-179555400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:179555000-179555400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
6	chr1:179555000-179555400	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr1:179555000-179555400	Bivalent Enhancer	Fetal Heart	heart
8	chr1:179555000-179555400	Bivalent Enhancer	Fetal Intestine Large	intestine
9	chr1:179555000-179555400	Bivalent Enhancer	Stomach Mucosa	stomach
10	chr1:179555000-179555600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
11	chr1:179555000-179555600	Flanking Active TSS	Brain Hippocampus Middle	brain
12	chr1:179555000-179555600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
13	chr1:179555000-179555800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
14	chr1:179555000-179555800	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr1:179555000-179555800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:179555000-179555800	Active TSS	Aorta	Aorta
17	chr1:179555000-179555800	Active TSS	Brain Germinal Matrix	brain
18	chr1:179555000-179555800	Active TSS	NH-A	brain
19	chr1:179555000-179556000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
20	chr1:179555000-179556000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:179555000-179556000	Active TSS	Brain Cingulate Gyrus	brain
22	chr1:179555000-179556000	Active TSS	Fetal Brain Female	brain
23	chr1:179555000-179556000	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr1:179555000-179556200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
25	chr1:179555000-179556200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
26	chr1:179555000-179556200	Enhancers	Fetal Brain Male	brain
27	chr1:179555000-179556200	Active TSS	Rectal Smooth Muscle	rectum
28	chr1:179555200-179555400	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr1:179555200-179555400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
30	chr1:179555200-179555400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:179555200-179555400	Active TSS	Colonic Mucosa	Colon
32	chr1:179555200-179555400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
33	chr1:179555200-179555400	Enhancers	Fetal Intestine Small	intestine
34	chr1:179555200-179555400	Active TSS	Ovary	ovary
35	chr1:179555200-179555400	Bivalent Enhancer	HUVEC	blood vessel
36	chr1:179555200-179555400	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
37	chr1:179555200-179555600	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:179555200-179555600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:179555200-179555600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:179555200-179555600	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr1:179555200-179555600	Bivalent/Poised TSS	Thymus	Thymus
42	chr1:179555200-179555800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:179555200-179555800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:179555200-179555800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:179555200-179555800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
46	chr1:179555200-179555800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:179555200-179555800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:179555200-179555800	Bivalent/Poised TSS	Fetal Stomach	stomach
49	chr1:179555200-179555800	Active TSS	Placenta Amnion	Placenta Amnion
50	chr1:179555200-179555800	Active TSS	Right Ventricle	heart

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