Variant report

Variant	rs12335657
Chromosome Location	chr9:110251605-110251606
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	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	SIN3AK20	chr9:110249660-110253043	MCF-7	breast:	n/a	n/a
4	CHD1	chr9:110251596-110251747	H1-hESC	embryonic stem cell:	n/a	n/a
5	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
6	RAD21	chr9:110250328-110251652	MCF-7	breast:	n/a	n/a
7	POLR2A	chr9:110251603-110252821	HCT-116	colon:	n/a	n/a
8	POLR2A	chr9:110249822-110252906	MCF10A-Er-Src	breast:	n/a	n/a
9	E2F6	chr9:110249233-110251929	H1-hESC	embryonic stem cell:	n/a	chr9:110251147-110251156
10	POLR2A	chr9:110250536-110252920	Hela-S3	cervix:	n/a	n/a
11	TBP	chr9:110251391-110251693	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr9:110251574-110251879	Hela-S3	cervix:	n/a	n/a
13	MAX	chr9:110251046-110252791	ECC-1	luminal epithelium:	n/a	chr9:110252538-110252547 chr9:110251148-110251158 chr9:110252561-110252571 chr9:110251925-110251935 chr9:110252169-110252178 chr9:110251779-110251789
14	POLR2A	chr9:110250111-110252852	MCF-7	breast:	n/a	n/a
15	POLR2A	chr9:110250505-110253064	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr9:110250532-110251764	H1-neurons	neurons:	n/a	n/a
17	E2F6	chr9:110250951-110251698	A549	lung:	n/a	chr9:110251147-110251156
18	HA-E2F1	chr9:110250487-110251866	MCF-7	breast:	n/a	chr9:110251147-110251156
19	ZBTB7A	chr9:110251159-110252000	ECC-1	luminal epithelium:	n/a	n/a
20	CTBP2	chr9:110249506-110251759	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr9:110248980-110252863	Hela-S3	cervix:	n/a	n/a
22	MAX	chr9:110250935-110251671	H1-hESC	embryonic stem cell:	n/a	chr9:110251148-110251158
23	MXI1	chr9:110250798-110251745	Hela-S3	cervix:	n/a	n/a
24	SMC3	chr9:110250668-110252912	Hela-S3	cervix:	n/a	n/a
25	MAX	chr9:110250838-110251622	H1-hESC	embryonic stem cell:	n/a	chr9:110251148-110251158 chr9:110250869-110250878
26	MAX	chr9:110251000-110251926	ECC-1	luminal epithelium:	n/a	chr9:110251148-110251158 chr9:110251779-110251789
27	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
28	MAX	chr9:110250304-110251923	A549	lung:	n/a	chr9:110251148-110251158 chr9:110251779-110251789 chr9:110250869-110250878
29	TCF7L2	chr9:110251375-110251716	Hela-S3	cervix:	n/a	n/a
30	ZBTB7A	chr9:110251572-110252040	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr9:110250903-110252300	K562	blood:	n/a	n/a
32	MAX	chr9:110249294-110251931	MCF-7	breast:	n/a	chr9:110251148-110251158 chr9:110251779-110251789 chr9:110250869-110250878
33	CHD2	chr9:110250598-110252882	Hela-S3	cervix:	n/a	chr9:110250929-110250939
34	POLR2A	chr9:110245600-110253991	IMR90	lung:	n/a	n/a
35	POLR2A	chr9:110248862-110252761	HCT-116	colon:	n/a	n/a
36	POLR2A	chr9:110250493-110253060	Hela-S3	cervix:	n/a	n/a
37	CHD1	chr9:110248044-110253182	IMR90	lung:	n/a	chr9:110250929-110250939
38	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
39	SMARCB1	chr9:110250018-110253034	Hela-S3	cervix:	n/a	chr9:110252538-110252547
40	HDAC2	chr9:110249261-110251706	MCF-7	breast:	n/a	n/a
41	TCF12	chr9:110250556-110251672	A549	lung:	n/a	n/a
42	HCFC1	chr9:110250307-110253159	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr9:110251148-110251621	H1-neurons	neurons:	n/a	n/a
44	GATA3	chr9:110249606-110251717	MCF-7	breast:	n/a	n/a
45	E2F6	chr9:110251001-110251910	H1-hESC	embryonic stem cell:	n/a	chr9:110251147-110251156
46	TAF1	chr9:110251575-110252331	ECC-1	luminal epithelium:	n/a	n/a
47	POLR2A	chr9:110250610-110252932	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr9:110249101-110253120	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:110250543..110252751-chr9:110679811..110682392,3	MCF-7	breast:
2	chr9:110193925..110197671-chr9:110251200..110254442,3	MCF-7	breast:
3	chr9:110190788..110193642-chr9:110249721..110252458,4	MCF-7	breast:
4	chr1:245134195..245134821-chr9:110251595..110252553,2	Hela-S3	cervix:
5	chr9:110189538..110195123-chr9:110249494..110254933,10	MCF-7	breast:
6	chr9:110246769..110253919-chr9:110298442..110306182,20	MCF-7	breast:
7	chr8:145109045..145111550-chr9:110250492..110251997,2	MCF-7	breast:

Variant related genes	Relation type
KLF4	TF binding region
ENSG00000226825	Chromatin interaction
ENSG00000263459	Chromatin interaction
ENSG00000227350	Chromatin interaction
ENSG00000272195	Chromatin interaction
ENSG00000178814	Chromatin interaction
ENSG00000222459	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10117763	0.88[EUR][1000 genomes]
rs10816519	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11788360	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11792359	1.00[EUR][1000 genomes]
rs11793219	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11794295	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11795298	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12336189	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12336214	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12340310	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12340462	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12345785	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12351651	1.00[EUR][1000 genomes]
rs12352260	0.94[EUR][1000 genomes]
rs12353064	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34651589	1.00[AMR][1000 genomes];1.00[EUR][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	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	nsv825028	chr9:110248596-110252543	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases
3	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
4	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
5	esv3403609	chr9:110251581-110252829	Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 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	chr9:110248600-110252800	Active TSS	Brain Cingulate Gyrus	brain
6	chr9:110249000-110251800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr9:110249000-110251800	Transcr. at gene 5' and 3'	Colonic Mucosa	Colon
8	chr9:110249000-110251800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
9	chr9:110249000-110252600	Active TSS	Osteobl	bone
10	chr9:110249000-110253200	Active TSS	Brain Substantia Nigra	brain
11	chr9:110249000-110253800	Active TSS	Brain Anterior Caudate	brain
12	chr9:110249200-110253000	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr9:110249200-110253400	Active TSS	Brain Angular Gyrus	brain
14	chr9:110249200-110254200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
15	chr9:110249400-110253800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr9:110249600-110251800	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:110249600-110251800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr9:110249600-110251800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr9:110249600-110252600	Active TSS	A549	lung
20	chr9:110249600-110252600	Active TSS	NHEK	skin
21	chr9:110249600-110252800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr9:110249600-110253200	Active TSS	Colon Smooth Muscle	Colon
23	chr9:110249600-110253200	Active TSS	NHDF-Ad	bronchial
24	chr9:110249600-110253400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
25	chr9:110249600-110253800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
26	chr9:110249600-110254000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
27	chr9:110249600-110254000	Active TSS	Placenta Amnion	Placenta Amnion
28	chr9:110249800-110251800	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
29	chr9:110249800-110251800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
30	chr9:110249800-110251800	Flanking Active TSS	Pancreas	Pancrea
31	chr9:110249800-110252600	Active TSS	Primary monocytes fromperipheralblood	blood
32	chr9:110249800-110252600	Active TSS	Monocytes-CD14+_RO01746	blood
33	chr9:110249800-110253000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr9:110249800-110253200	Active TSS	HSMM	muscle
35	chr9:110250000-110251800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
36	chr9:110250000-110251800	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr9:110250000-110251800	Enhancers	Fetal Heart	heart
38	chr9:110250000-110252400	Active TSS	Duodenum Mucosa	Duodenum
39	chr9:110250000-110253800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr9:110250200-110253800	Active TSS	Left Ventricle	heart
41	chr9:110250200-110254000	Active TSS	Rectal Smooth Muscle	rectum
42	chr9:110250400-110251800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr9:110250400-110251800	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
44	chr9:110250400-110251800	Flanking Active TSS	Liver	Liver
45	chr9:110250400-110252400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr9:110250400-110252400	Active TSS	Adipose Nuclei	Adipose
47	chr9:110250400-110252600	Active TSS	Muscle Satellite Cultured Cells	--
48	chr9:110250400-110252800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr9:110250400-110253000	Active TSS	HSMMtube	muscle
50	chr9:110250400-110254000	Active TSS	Aorta	Aorta

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