Variant report

Variant	rs564287500
Chromosome Location	chr3:53169060-53169061
allele	A/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	CTCF	chr3:53168462-53169391	SK-N-SH	brain:	n/a	chr3:53168894-53168912 chr3:53168896-53168917 chr3:53168898-53168905 chr3:53168895-53168911 chr3:53168897-53168910
2	TBP	chr3:53168708-53169086	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAZ	chr3:53168584-53169080	Hela-S3	cervix:	n/a	n/a
4	CHD2	chr3:53168742-53169072	Hela-S3	cervix:	n/a	n/a
5	TEAD4	chr3:53168721-53169090	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr3:53168628-53169140	HepG2	liver:	n/a	chr3:53168894-53168912 chr3:53168896-53168917 chr3:53168898-53168905 chr3:53168895-53168911 chr3:53168897-53168910
7	CTCF	chr3:53168534-53169190	HCT-116	colon:	n/a	chr3:53168894-53168912 chr3:53168896-53168917 chr3:53168898-53168905 chr3:53168895-53168911 chr3:53168897-53168910
8	TEAD4	chr3:53168689-53169121	H1-hESC	embryonic stem cell:	n/a	n/a
9	EP300	chr3:53168309-53169157	ECC-1	luminal epithelium:	n/a	n/a
10	CTCF	chr3:53168659-53169084	K562	blood:	n/a	chr3:53168894-53168912 chr3:53168896-53168917 chr3:53168898-53168905 chr3:53168895-53168911 chr3:53168897-53168910
11	CTCF	chr3:53168920-53169070	RPTEC	kidney:	n/a	n/a
12	BRCA1	chr3:53168897-53169094	HepG2	liver:	n/a	n/a
13	EBF1	chr3:53168749-53169159	GM12878	blood:	n/a	n/a
14	ZNF143	chr3:53168723-53169257	GM12878	blood:	n/a	n/a
15	RCOR1	chr3:53168794-53169140	GM12878	blood:	n/a	n/a
16	CTCF	chr3:53168709-53169062	GM19240	blood:	n/a	chr3:53168894-53168912 chr3:53168896-53168917 chr3:53168898-53168905 chr3:53168895-53168911 chr3:53168897-53168910
17	USF2	chr3:53168756-53169069	Hela-S3	cervix:	n/a	n/a
18	WRNIP1	chr3:53168779-53169281	GM12878	blood:	n/a	n/a
19	CTCF	chr3:53168652-53169141	GM12878	blood:	n/a	chr3:53168894-53168912 chr3:53168896-53168917 chr3:53168898-53168905 chr3:53168895-53168911 chr3:53168897-53168910
20	CTCF	chr3:53168726-53169079	K562	blood:	n/a	chr3:53168894-53168912 chr3:53168896-53168917 chr3:53168898-53168905 chr3:53168895-53168911 chr3:53168897-53168910
21	RAD21	chr3:53168499-53169262	HCT-116	colon:	n/a	chr3:53168895-53168914 chr3:53168896-53168905 chr3:53168896-53168910
22	CTCF	chr3:53168734-53169064	NHEK	skin:	n/a	chr3:53168894-53168912 chr3:53168896-53168917 chr3:53168898-53168905 chr3:53168895-53168911 chr3:53168897-53168910
23	MYC	chr3:53168772-53169074	MCF10A-Er-Src	breast:	n/a	n/a
24	NFIC	chr3:53168348-53169213	ECC-1	luminal epithelium:	n/a	n/a
25	ZNF143	chr3:53168719-53169316	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr3:53168653-53169129	H1-hESC	embryonic stem cell:	n/a	chr3:53168894-53168912 chr3:53168896-53168917 chr3:53168898-53168905 chr3:53168895-53168911 chr3:53168897-53168910
27	RAD21	chr3:53168659-53169179	HepG2	liver:	n/a	chr3:53168895-53168914 chr3:53168896-53168905 chr3:53168896-53168910
28	CTCF	chr3:53168726-53169064	GM12892	blood:	n/a	chr3:53168894-53168912 chr3:53168896-53168917 chr3:53168898-53168905 chr3:53168895-53168911 chr3:53168897-53168910
29	ELK1	chr3:53168892-53169092	GM12878	blood:	n/a	n/a
30	MAX	chr3:53168786-53169194	GM12878	blood:	n/a	n/a
31	RAD21	chr3:53168629-53169123	A549	lung:	n/a	chr3:53168895-53168914 chr3:53168896-53168905 chr3:53168896-53168910
32	ZNF143	chr3:53168737-53169239	Hela-S3	cervix:	n/a	n/a
33	CTCF	chr3:53168712-53169070	A549	lung:	n/a	chr3:53168894-53168912 chr3:53168896-53168917 chr3:53168898-53168905 chr3:53168895-53168911 chr3:53168897-53168910
34	MAX	chr3:53168736-53169227	H1-hESC	embryonic stem cell:	n/a	n/a
35	ZNF143	chr3:53168762-53169249	K562	blood:	n/a	n/a
36	MAX	chr3:53168477-53169144	ECC-1	luminal epithelium:	n/a	n/a
37	MAZ	chr3:53168759-53169089	GM12878	blood:	n/a	n/a
38	RCOR1	chr3:53168770-53169220	HepG2	liver:	n/a	n/a
39	RAD21	chr3:53168694-53169207	MCF-7	breast:	n/a	chr3:53168895-53168914 chr3:53168896-53168905 chr3:53168896-53168910
40	RAD21	chr3:53168651-53169120	SK-N-SH_RA	brain:	n/a	chr3:53168895-53168914 chr3:53168896-53168905 chr3:53168896-53168910
41	RAD21	chr3:53168698-53169130	Hela-S3	cervix:	n/a	chr3:53168895-53168914 chr3:53168896-53168905 chr3:53168896-53168910
42	TBL1XR1	chr3:53168790-53169163	GM12878	blood:	n/a	n/a
43	RAD21	chr3:53168601-53169156	H1-hESC	embryonic stem cell:	n/a	chr3:53168895-53168914 chr3:53168896-53168905 chr3:53168896-53168910
44	CTCF	chr3:53168667-53169102	T-47D	breast:	n/a	chr3:53168894-53168912 chr3:53168896-53168917 chr3:53168898-53168905 chr3:53168895-53168911 chr3:53168897-53168910
45	YY1	chr3:53168690-53169081	GM12892	blood:	n/a	chr3:53168920-53168934
46	SMC3	chr3:53168513-53169299	SK-N-SH	brain:	n/a	chr3:53168896-53168910 chr3:53168655-53168665
47	RAD21	chr3:53168666-53169083	HepG2	liver:	n/a	chr3:53168895-53168914 chr3:53168896-53168905 chr3:53168896-53168910
48	GTF2F1	chr3:53168702-53169119	Hela-S3	cervix:	n/a	n/a
49	CTCF	chr3:53168655-53169104	ECC-1	luminal epithelium:	n/a	chr3:53168894-53168912 chr3:53168896-53168917 chr3:53168898-53168905 chr3:53168895-53168911 chr3:53168897-53168910
50	SMC3	chr3:53168720-53169182	HepG2	liver:	n/a	chr3:53168896-53168910

No.	Distal block	Cell Line	Cell type
1	chr3:53168443..53169334-chr3:53229545..53230512,6	MCF-7	breast:
2	chr3:53160337..53170540-chr3:53189028..53198029,25	MCF-7	breast:
3	chr3:53168415..53169413-chr3:53219615..53220145,2	MCF-7	breast:
4	chr3:53163343..53166728-chr3:53167224..53170479,4	MCF-7	breast:
5	chr3:53168393..53169379-chr3:53229728..53230708,4	MCF-7	breast:
6	chr3:53168501..53169455-chr3:53194754..53195688,3	MCF-7	breast:
7	chr3:53167017..53169952-chr3:53191720..53194469,2	K562	blood:

Variant related genes	Relation type
RFT1	TF binding region
ENSG00000163933	Chromatin interaction
ENSG00000163932	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

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	nsv590356	chr3:53134098-53170500	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
2	nsv460553	chr3:53147576-53185061	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
3	nsv590357	chr3:53147576-53185061	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
4	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv3381848	chr3:53167712-53172310	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53164800-53170600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:53165000-53169800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:53165000-53176200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:53165000-53176400	Weak transcription	Aorta	Aorta
5	chr3:53165200-53169800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:53165400-53173800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:53165400-53176000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr3:53165600-53169200	Weak transcription	Brain Anterior Caudate	brain
9	chr3:53165600-53169600	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:53165600-53170800	Weak transcription	Fetal Thymus	thymus
11	chr3:53165600-53173400	Weak transcription	Gastric	stomach
12	chr3:53165600-53174200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:53165600-53174200	Weak transcription	Fetal Heart	heart
14	chr3:53165600-53174200	Weak transcription	Left Ventricle	heart
15	chr3:53165600-53174600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:53165600-53177800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:53165600-53181400	Weak transcription	Spleen	Spleen
18	chr3:53165800-53170600	Weak transcription	GM12878-XiMat	blood
19	chr3:53165800-53175400	Weak transcription	Placenta	Placenta
20	chr3:53166200-53174600	Weak transcription	Primary B cells from cord blood	blood
21	chr3:53166400-53170200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:53166400-53171200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:53167200-53174400	Weak transcription	HMEC	breast
24	chr3:53167600-53169200	Enhancers	Liver	Liver
25	chr3:53167600-53170200	Enhancers	Adipose Nuclei	Adipose
26	chr3:53168200-53169200	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr3:53168200-53170000	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr3:53168400-53169200	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr3:53168400-53169400	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr3:53168400-53169400	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr3:53168400-53169400	Enhancers	Hela-S3	cervix
32	chr3:53168400-53169400	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr3:53168400-53170000	Enhancers	Duodenum Mucosa	Duodenum
34	chr3:53168400-53170000	Enhancers	Stomach Mucosa	stomach
35	chr3:53168400-53170200	Weak transcription	HepG2	liver
36	chr3:53168400-53170800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr3:53168600-53169200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:53168600-53169200	Enhancers	Primary B cells from peripheral blood	blood
39	chr3:53168600-53169200	Enhancers	Primary T cells fromperipheralblood	blood
40	chr3:53168600-53169200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:53168600-53169200	Enhancers	Brain Hippocampus Middle	brain
42	chr3:53168600-53169200	Enhancers	Colon Smooth Muscle	Colon
43	chr3:53168600-53169200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr3:53168600-53169200	Enhancers	Fetal Intestine Large	intestine
45	chr3:53168600-53169200	Enhancers	Fetal Lung	lung
46	chr3:53168600-53169200	Enhancers	Pancreas	Pancrea
47	chr3:53168600-53169200	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr3:53168600-53169200	Enhancers	Right Ventricle	heart
49	chr3:53168600-53169200	Enhancers	Stomach Smooth Muscle	stomach
50	chr3:53168600-53169400	Enhancers	Primary monocytes fromperipheralblood	blood

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