Variant report

Variant	rs10117763
Chromosome Location	chr9:110252870-110252871
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	MAX	chr9:110249578-110253080	A549	lung:	n/a	chr9:110252538-110252547 chr9:110251148-110251158 chr9:110252561-110252571 chr9:110251925-110251935 chr9:110252169-110252178 chr9:110251779-110251789 chr9:110250869-110250878
2	POLR2A	chr9:110250668-110253189	MCF10A-Er-Src	breast:	n/a	n/a
3	RAD21	chr9:110251920-110252955	IMR90	lung:	n/a	n/a
4	SIN3AK20	chr9:110249660-110253043	MCF-7	breast:	n/a	n/a
5	E2F6	chr9:110252086-110252986	A549	lung:	n/a	n/a
6	MAZ	chr9:110250243-110253317	IMR90	lung:	n/a	chr9:110252538-110252547 chr9:110251148-110251158 chr9:110252561-110252571 chr9:110251925-110251935 chr9:110252169-110252178 chr9:110251779-110251789 chr9:110250869-110250878
7	POLR2A	chr9:110252215-110252882	U87	brain:	n/a	n/a
8	FOSL2	chr9:110252276-110252904	SK-N-SH	brain:	n/a	chr9:110252538-110252547 chr9:110252536-110252548 chr9:110252394-110252402
9	BCL3	chr9:110252248-110252990	A549	lung:	n/a	n/a
10	MAX	chr9:110251939-110252933	H1-hESC	embryonic stem cell:	n/a	chr9:110252538-110252547 chr9:110252561-110252571 chr9:110252169-110252178
11	POLR2A	chr9:110249822-110252906	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr9:110252005-110252928	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr9:110250536-110252920	Hela-S3	cervix:	n/a	n/a
14	MAX	chr9:110251928-110252993	A549	lung:	n/a	chr9:110252538-110252547 chr9:110252561-110252571 chr9:110252169-110252178
15	POLR2A	chr9:110252285-110253101	U87	brain:	n/a	n/a
16	E2F6	chr9:110251928-110252944	H1-hESC	embryonic stem cell:	n/a	chr9:110251975-110251985
17	CTCF	chr9:110252760-110252910	AoAF	blood vessel:	n/a	n/a
18	HA-E2F1	chr9:110252218-110252941	MCF-7	breast:	n/a	chr9:110252493-110252504
19	RFX5	chr9:110251966-110252871	Hela-S3	cervix:	n/a	chr9:110252169-110252178 chr9:110252168-110252183 chr9:110252168-110252183 chr9:110252168-110252183 chr9:110252166-110252180 chr9:110252167-110252184
20	POLR2A	chr9:110250505-110253064	HUVEC	blood vessel:	n/a	n/a
21	JUND	chr9:110252072-110252881	SK-N-SH	brain:	n/a	chr9:110252077-110252086 chr9:110252538-110252547 chr9:110252142-110252151 chr9:110252536-110252548 chr9:110252536-110252547 chr9:110252394-110252402
22	TEAD4	chr9:110252836-110253208	H1-hESC	embryonic stem cell:	n/a	n/a
23	E2F6	chr9:110251684-110252934	K562	blood:	n/a	chr9:110251975-110251985
24	E2F6	chr9:110251983-110253004	H1-hESC	embryonic stem cell:	n/a	n/a
25	CHD1	chr9:110252336-110252921	H1-hESC	embryonic stem cell:	n/a	n/a
26	SMC3	chr9:110250668-110252912	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr9:110252279-110253101	U87	brain:	n/a	n/a
28	MYC	chr9:110251909-110253043	A549	lung:	n/a	chr9:110252538-110252547 chr9:110252561-110252571 chr9:110251925-110251935 chr9:110252169-110252178
29	MAX	chr9:110250700-110252919	Hela-S3	cervix:	n/a	chr9:110252538-110252547 chr9:110251148-110251158 chr9:110252561-110252571 chr9:110251925-110251935 chr9:110252169-110252178 chr9:110251779-110251789 chr9:110250869-110250878
30	CTCF	chr9:110252760-110252910	BJ	skin:	n/a	n/a
31	MAX	chr9:110251933-110252900	MCF-7	breast:	n/a	chr9:110252538-110252547 chr9:110252561-110252571 chr9:110252169-110252178
32	BACH1	chr9:110252376-110252937	H1-hESC	embryonic stem cell:	n/a	chr9:110252535-110252549
33	REST	chr9:110251947-110253059	H1-neurons	neurons:	n/a	chr9:110252721-110252739
34	GATA3	chr9:110251943-110252928	A549	lung:	n/a	n/a
35	CHD2	chr9:110250598-110252882	Hela-S3	cervix:	n/a	chr9:110250929-110250939
36	POLR2A	chr9:110245600-110253991	IMR90	lung:	n/a	n/a
37	POLR2A	chr9:110250493-110253060	Hela-S3	cervix:	n/a	n/a
38	CHD1	chr9:110248044-110253182	IMR90	lung:	n/a	chr9:110250929-110250939
39	RAD21	chr9:110251940-110252889	Hela-S3	cervix:	n/a	n/a
40	MAZ	chr9:110250615-110252891	Hela-S3	cervix:	n/a	chr9:110252538-110252547 chr9:110251148-110251158 chr9:110252561-110252571 chr9:110251925-110251935 chr9:110252169-110252178 chr9:110251779-110251789 chr9:110250869-110250878
41	ZNF384	chr9:110252770-110252928	K562	blood:	n/a	n/a
42	SMARCB1	chr9:110250018-110253034	Hela-S3	cervix:	n/a	chr9:110252538-110252547
43	TEAD4	chr9:110252793-110253240	H1-hESC	embryonic stem cell:	n/a	n/a
44	HCFC1	chr9:110250307-110253159	Hela-S3	cervix:	n/a	n/a
45	TCF12	chr9:110251879-110253039	A549	lung:	n/a	chr9:110252270-110252277
46	POLR2A	chr9:110250610-110252932	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr9:110249101-110253120	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:110045521..110048079-chr9:110251760..110253947,2	MCF-7	breast:
2	chr9:110193925..110197671-chr9:110251200..110254442,3	MCF-7	breast:
3	chr9:110251912..110253723-chrX:47002554..47004950,2	MCF-7	breast:
4	chr9:110189538..110195123-chr9:110249494..110254933,10	MCF-7	breast:
5	chr9:110246769..110253919-chr9:110298442..110306182,20	MCF-7	breast:
6	chr8:101224274..101226776-chr9:110251718..110253373,2	MCF-7	breast:
7	chr16:89988575..89990110-chr9:110251839..110254629,2	MCF-7	breast:

Variant related genes	Relation type
KLF4	TF binding region
ENSG00000182872	Chromatin interaction
ENSG00000263459	Chromatin interaction
ENSG00000104450	Chromatin interaction
ENSG00000227350	Chromatin interaction
ENSG00000119318	Chromatin interaction
ENSG00000147123	Chromatin interaction
ENSG00000259006	Chromatin interaction
ENSG00000226825	Chromatin interaction
ENSG00000258947	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10816519	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10978813	1.00[CEU][hapmap]
rs10978814	1.00[CEU][hapmap]
rs10978817	1.00[CEU][hapmap]
rs11788360	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11792359	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11793219	0.88[EUR][1000 genomes]
rs11794295	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11795298	0.88[EUR][1000 genomes]
rs12005490	1.00[CEU][hapmap]
rs12335657	0.88[EUR][1000 genomes]
rs12336189	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12336214	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12340310	0.88[EUR][1000 genomes]
rs12340462	0.88[EUR][1000 genomes]
rs12345785	0.88[EUR][1000 genomes]
rs12351651	0.88[EUR][1000 genomes]
rs12352260	0.82[EUR][1000 genomes]
rs12353064	0.88[EUR][1000 genomes]
rs34651589	0.88[EUR][1000 genomes]
rs7024696	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530948	chr9:109760752-110413602	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv3357054	chr9:110250656-110253504	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	esv3404298	chr9:110250731-110252929	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110246200-110253800	Active TSS	Right Atrium	heart
2	chr9:110247200-110254000	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr9:110247400-110253800	Active TSS	Psoas Muscle	Psoas
4	chr9:110248400-110254200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr9:110249000-110253200	Active TSS	Brain Substantia Nigra	brain
6	chr9:110249000-110253800	Active TSS	Brain Anterior Caudate	brain
7	chr9:110249200-110253000	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr9:110249200-110253400	Active TSS	Brain Angular Gyrus	brain
9	chr9:110249200-110254200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr9:110249400-110253800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr9:110249600-110253200	Active TSS	Colon Smooth Muscle	Colon
12	chr9:110249600-110253200	Active TSS	NHDF-Ad	bronchial
13	chr9:110249600-110253400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr9:110249600-110253800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
15	chr9:110249600-110254000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
16	chr9:110249600-110254000	Active TSS	Placenta Amnion	Placenta Amnion
17	chr9:110249800-110253000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr9:110249800-110253200	Active TSS	HSMM	muscle
19	chr9:110250000-110253800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:110250200-110253800	Active TSS	Left Ventricle	heart
21	chr9:110250200-110254000	Active TSS	Rectal Smooth Muscle	rectum
22	chr9:110250400-110253000	Active TSS	HSMMtube	muscle
23	chr9:110250400-110254000	Active TSS	Aorta	Aorta
24	chr9:110250400-110254000	Active TSS	Ovary	ovary
25	chr9:110250600-110253200	Active TSS	NHLF	lung
26	chr9:110251000-110254000	Active TSS	Esophagus	oesophagus
27	chr9:110251200-110254000	Active TSS	Gastric	stomach
28	chr9:110251400-110253000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr9:110251400-110254000	Active TSS	Right Ventricle	heart
30	chr9:110251600-110253000	Active TSS	H9 Cell Line	embryonic stem cell
31	chr9:110251600-110253000	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr9:110251600-110253600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr9:110251600-110253800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr9:110251600-110253800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr9:110251600-110254000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr9:110251600-110254200	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr9:110251800-110253000	Bivalent/Poised TSS	Thymus	Thymus
38	chr9:110251800-110253800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr9:110251800-110253800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
40	chr9:110251800-110254000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:110252200-110253200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr9:110252400-110253000	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:110252400-110253000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:110252400-110253000	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
45	chr9:110252400-110253000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
46	chr9:110252400-110253000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
47	chr9:110252400-110253000	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
48	chr9:110252400-110253000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
49	chr9:110252400-110253000	Flanking Bivalent TSS/Enh	HepG2	liver
50	chr9:110252400-110253000	Flanking Active TSS	HMEC	breast

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