Variant report

Variant	rs112166522
Chromosome Location	chr9:17135015-17135016
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	POLR2A	chr9:17134684-17135405	HL-60	blood:	n/a	n/a
2	TAF1	chr9:17134869-17135229	GM12892	blood:	n/a	n/a
3	REST	chr9:17134763-17135101	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr9:17134584-17135791	H1-hESC	embryonic stem cell:	n/a	n/a
5	TAF7	chr9:17134696-17135237	H1-hESC	embryonic stem cell:	n/a	n/a
6	MYC	chr9:17134911-17135135	HepG2	liver:	n/a	n/a
7	POLR2A	chr9:17134513-17135784	ECC-1	luminal epithelium:	n/a	n/a
8	MYBL2	chr9:17134767-17135078	HepG2	liver:	n/a	n/a
9	BRCA1	chr9:17134617-17135090	Hela-S3	cervix:	n/a	n/a
10	TCF12	chr9:17134592-17135439	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr9:17134778-17135250	HCT-116	colon:	n/a	n/a
12	HA-E2F1	chr9:17134686-17135603	Hela-S3	cervix:	n/a	chr9:17134779-17134786 chr9:17134953-17134965 chr9:17134779-17134786 chr9:17134779-17134786 chr9:17134953-17134964 chr9:17134957-17134964 chr9:17135482-17135496 chr9:17134957-17134964 chr9:17135566-17135576 chr9:17134775-17134787 chr9:17134957-17134964 chr9:17134956-17134965 chr9:17134778-17134787 chr9:17135487-17135494
13	POLR2A	chr9:17134448-17135841	Hela-S3	cervix:	n/a	n/a
14	MAX	chr9:17134383-17135869	A549	lung:	n/a	chr9:17135562-17135572
15	CTCF	chr9:17135000-17135150	HUVEC	blood vessel:	n/a	n/a
16	GATA1	chr9:17133794-17135869	PBDE	blood:	n/a	chr9:17134499-17134506 chr9:17134125-17134146 chr9:17134128-17134144 chr9:17134128-17134144
17	HEY1	chr9:17134862-17135196	HepG2	liver:	n/a	n/a
18	YY1	chr9:17134782-17135519	SK-N-SH_RA	brain:	n/a	n/a
19	E2F6	chr9:17134508-17135460	A549	lung:	n/a	chr9:17134779-17134786 chr9:17134953-17134965 chr9:17134779-17134786 chr9:17134779-17134786 chr9:17134778-17134786 chr9:17134957-17134964 chr9:17134957-17134964 chr9:17134775-17134787 chr9:17134957-17134964 chr9:17134956-17134965 chr9:17134778-17134787
20	POLR2A	chr9:17134707-17135706	GM12892	blood:	n/a	n/a
21	SP1	chr9:17134684-17135415	A549	lung:	n/a	n/a
22	FOXA2	chr9:17134588-17135230	A549	lung:	n/a	n/a
23	POLR2A	chr9:17134378-17135856	Hela-S3	cervix:	n/a	n/a
24	TAF1	chr9:17134736-17135190	HepG2	liver:	n/a	n/a
25	GATA2	chr9:17134996-17135807	HUVEC	blood vessel:	n/a	n/a
26	RFX5	chr9:17134508-17136086	Hela-S3	cervix:	n/a	n/a
27	YY1	chr9:17134861-17135532	NT2-D1	testis:	n/a	n/a
28	USF1	chr9:17134697-17135142	A549	lung:	n/a	n/a
29	POLR2A	chr9:17134603-17135340	PFSK-1	brain:	n/a	n/a
30	POLR2A	chr9:17134882-17135197	HepG2	liver:	n/a	n/a
31	YY1	chr9:17134910-17135212	GM12892	blood:	n/a	n/a
32	YY1	chr9:17134864-17135242	HepG2	liver:	n/a	n/a
33	E2F4	chr9:17134434-17135554	Hela-S3	cervix:	n/a	chr9:17134779-17134786 chr9:17134953-17134965 chr9:17134779-17134786 chr9:17134779-17134786 chr9:17134778-17134786 chr9:17134957-17134964 chr9:17135482-17135496 chr9:17134957-17134964 chr9:17134775-17134787 chr9:17134957-17134964 chr9:17134956-17134965 chr9:17134778-17134787 chr9:17135487-17135494
34	RCOR1	chr9:17134263-17136162	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr9:17134687-17135579	HL-60	blood:	n/a	n/a
36	POLR2A	chr9:17134628-17135297	U87	brain:	n/a	n/a
37	POLR2A	chr9:17134560-17135907	Hela-S3	cervix:	n/a	n/a
38	GATA3	chr9:17135006-17135326	T-47D	breast:	n/a	n/a
39	USF1	chr9:17134779-17135145	SK-N-SH_RA	brain:	n/a	n/a
40	HA-E2F1	chr9:17134483-17135230	MCF-7	breast:	n/a	chr9:17134779-17134786 chr9:17134953-17134965 chr9:17134779-17134786 chr9:17134779-17134786 chr9:17134953-17134964 chr9:17134957-17134964 chr9:17134957-17134964 chr9:17134775-17134787 chr9:17134957-17134964 chr9:17134956-17134965 chr9:17134778-17134787
41	E2F6	chr9:17134197-17135850	A549	lung:	n/a	chr9:17134779-17134786 chr9:17134953-17134965 chr9:17134779-17134786 chr9:17134779-17134786 chr9:17134778-17134786 chr9:17134957-17134964 chr9:17135482-17135496 chr9:17134957-17134964 chr9:17135566-17135576 chr9:17134775-17134787 chr9:17134957-17134964 chr9:17134956-17134965 chr9:17134778-17134787 chr9:17135487-17135494
42	USF1	chr9:17134721-17135335	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr9:17134693-17135239	A549	lung:	n/a	n/a
44	POLR2A	chr9:17134673-17135983	IMR90	lung:	n/a	n/a
45	POLR2A	chr9:17134595-17135771	PFSK-1	brain:	n/a	n/a
46	POLR2A	chr9:17134437-17135754	Raji	blood:	n/a	n/a
47	MAZ	chr9:17134928-17135191	HepG2	liver:	n/a	n/a
48	POLR2A	chr9:17134552-17135835	GM12892	blood:	n/a	n/a
49	CTBP2	chr9:17134341-17135818	H1-hESC	embryonic stem cell:	n/a	n/a
50	YY1	chr9:17134823-17135566	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:692813..693544-chr9:17134998..17135501,2	NB4	blood:
2	chr5:43121428..43122109-chr9:17134722..17135406,2	Hela-S3	cervix:
3	chr1:11969364..11970234-chr9:17134620..17135236,2	Hela-S3	cervix:
4	chr15:23810837..23811461-chr9:17134816..17135417,2	NB4	blood:
5	chr13:49549584..49550165-chr9:17134587..17135235,2	NB4	blood:

Variant related genes	Relation type
CNTLN	TF binding region
ENSG00000172262	Chromatin interaction
ENSG00000102531	Chromatin interaction
ENSG00000201801	Chromatin interaction
ENSG00000179455	Chromatin interaction
ENSG00000112685	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	esv2764141	chr9:16903446-17351711	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv892657	chr9:17008137-17223492	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv892658	chr9:17041557-17532840	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv1023525	chr9:17121773-17236072	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv892659	chr9:17130360-17236376	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv892660	chr9:17134245-17269437	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv892661	chr9:17134245-17532840	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17134200-17136400	Active TSS	Fetal Brain Female	brain
2	chr9:17134400-17135200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr9:17134400-17135800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr9:17134400-17136000	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr9:17134400-17136000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr9:17134400-17136000	Active TSS	Brain Hippocampus Middle	brain
7	chr9:17134400-17136000	Active TSS	Brain Substantia Nigra	brain
8	chr9:17134400-17136200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr9:17134400-17136200	Active TSS	Brain Anterior Caudate	brain
10	chr9:17134400-17136400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:17134400-17136400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:17134600-17135200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr9:17134600-17135200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr9:17134600-17135400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr9:17134600-17135600	Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr9:17134600-17135600	Flanking Active TSS	Placenta	Placenta
17	chr9:17134600-17135600	Active TSS	Small Intestine	intestine
18	chr9:17134600-17135800	Flanking Active TSS	Colonic Mucosa	Colon
19	chr9:17134600-17136000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr9:17134600-17136000	Active TSS	Pancreas	Pancrea
21	chr9:17134600-17136000	Active TSS	Psoas Muscle	Psoas
22	chr9:17134600-17136200	Active TSS	H9 Cell Line	embryonic stem cell
23	chr9:17134600-17136200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr9:17134600-17136200	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr9:17134600-17136200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr9:17134600-17136200	Active TSS	Aorta	Aorta
27	chr9:17134600-17136200	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr9:17134600-17136200	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr9:17134600-17136200	Active TSS	Right Atrium	heart
30	chr9:17134600-17136200	Active TSS	HSMM	muscle
31	chr9:17134600-17136200	Active TSS	HSMMtube	muscle
32	chr9:17134600-17136400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr9:17134600-17136400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr9:17134600-17136400	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr9:17134800-17135200	Active TSS	Brain Germinal Matrix	brain
36	chr9:17134800-17135200	Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr9:17134800-17135200	Flanking Active TSS	Spleen	Spleen
38	chr9:17134800-17135800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:17134800-17135800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr9:17134800-17135800	Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr9:17134800-17135800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr9:17134800-17135800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr9:17134800-17135800	Active TSS	Liver	Liver
44	chr9:17134800-17135800	Active TSS	Brain Cingulate Gyrus	brain
45	chr9:17134800-17135800	Active TSS	Fetal Heart	heart
46	chr9:17134800-17135800	Active TSS	Placenta Amnion	Placenta Amnion
47	chr9:17134800-17135800	Active TSS	Stomach Mucosa	stomach
48	chr9:17134800-17135800	Active TSS	NH-A	brain
49	chr9:17134800-17136000	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr9:17134800-17136000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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