Variant report

Variant	rs3208472
Chromosome Location	chr9:97766550-97766551
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	TCF12	chr9:97766385-97767254	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr9:97766270-97766655	HUVEC	blood vessel:	n/a	n/a
3	SIN3AK20	chr9:97766218-97767008	MCF-7	breast:	n/a	n/a
4	GATA3	chr9:97766040-97766815	MCF-7	breast:	n/a	n/a
5	CTCF	chr9:97766440-97766590	BJ	skin:	n/a	n/a
6	SIN3AK20	chr9:97766440-97766967	A549	lung:	n/a	n/a
7	ARID3A	chr9:97766146-97766825	HepG2	liver:	n/a	n/a
8	SMC3	chr9:97766199-97766991	Hela-S3	cervix:	n/a	n/a
9	MAX	chr9:97766258-97767040	SK-N-SH	brain:	n/a	n/a
10	CTCF	chr9:97766540-97766690	SK-N-SH_RA	brain:	n/a	n/a
11	ATF3	chr9:97766192-97766782	A549	lung:	n/a	n/a
12	RAD21	chr9:97766239-97766859	Hela-S3	cervix:	n/a	chr9:97766704-97766714
13	CTCF	chr9:97766440-97766590	NHDF-neo	bronchial:	n/a	n/a
14	RAD21	chr9:97766289-97767005	SK-N-SH_RA	brain:	n/a	chr9:97766704-97766714
15	EP300	chr9:97766155-97767085	ECC-1	luminal epithelium:	n/a	chr9:97766680-97766696
16	UBTF	chr9:97766237-97767980	K562	blood:	n/a	n/a
17	CTCF	chr9:97766460-97766610	HMF	breast:	n/a	n/a
18	MYC	chr9:97766397-97766614	MCF10A-Er-Src	breast:	n/a	n/a
19	JUND	chr9:97766178-97766552	H1-hESC	embryonic stem cell:	n/a	n/a
20	ETS1	chr9:97766279-97766848	A549	lung:	n/a	chr9:97766716-97766727
21	MYC	chr9:97766335-97766979	K562	blood:	n/a	n/a
22	MXI1	chr9:97766181-97766727	K562	blood:	n/a	n/a
23	RAD21	chr9:97766218-97766997	MCF-7	breast:	n/a	chr9:97766704-97766714
24	POLR2A	chr9:97766117-97768000	ProgFib	skin:	n/a	n/a
25	CTCF	chr9:97766420-97766570	HMEC	breast:	n/a	n/a
26	CEBPB	chr9:97766356-97766596	Hela-S3	cervix:	n/a	n/a
27	TBP	chr9:97766342-97767174	HepG2	liver:	n/a	n/a
28	MAX	chr9:97766261-97767827	HepG2	liver:	n/a	chr9:97767735-97767745
29	RCOR1	chr9:97766239-97766912	Hela-S3	cervix:	n/a	n/a
30	MAFK	chr9:97766453-97766819	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr9:97766405-97767000	HCT-116	colon:	n/a	n/a
32	BRCA1	chr9:97766064-97766730	Hela-S3	cervix:	n/a	n/a
33	RFX5	chr9:97766088-97766987	HepG2	liver:	n/a	n/a
34	SIX5	chr9:97765918-97766734	A549	lung:	n/a	n/a
35	HEY1	chr9:97766234-97766996	HepG2	liver:	n/a	chr9:97766677-97766692 chr9:97766679-97766694
36	RAD21	chr9:97766342-97766984	H1-hESC	embryonic stem cell:	n/a	chr9:97766704-97766714
37	MAX	chr9:97766388-97766894	A549	lung:	n/a	n/a
38	POLR2A	chr9:97765950-97767012	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr9:97766071-97767003	ECC-1	luminal epithelium:	n/a	n/a
40	TAF1	chr9:97766312-97766612	SK-N-SH	brain:	n/a	n/a
41	CTCF	chr9:97766400-97766550	HRE	kidney:	n/a	n/a
42	CTCF	chr9:97766400-97766550	HA-sp	spinal cord:	n/a	n/a
43	BACH1	chr9:97766534-97766861	H1-hESC	embryonic stem cell:	n/a	n/a
44	HA-E2F1	chr9:97766356-97767869	Hela-S3	cervix:	n/a	chr9:97767133-97767142 chr9:97767139-97767151 chr9:97767538-97767547 chr9:97767164-97767173 chr9:97766836-97766843 chr9:97766836-97766843 chr9:97766903-97766915 chr9:97767512-97767521 chr9:97766836-97766843 chr9:97767691-97767700
45	CTCF	chr9:97766400-97766550	AG04449	skin:	n/a	n/a
46	SP1	chr9:97765773-97767001	A549	lung:	n/a	chr9:97766690-97766699
47	HCFC1	chr9:97766389-97766884	K562	blood:	n/a	n/a
48	MAZ	chr9:97766396-97766984	Hela-S3	cervix:	n/a	n/a
49	CTCF	chr9:97766400-97766550	HPAF	blood vessel:	n/a	n/a
50	POLR2A	chr9:97765858-97769286	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:97316005..97317970-chr9:97766242..97767931,2	MCF-7	breast:
2	chr9:97671639..97694679-chr9:97760418..97786060,142	MCF-7	breast:
3	chr9:97763979..97769403-chr9:97805439..97812937,10	MCF-7	breast:
4	chr9:97765581..97769970-chr9:97809027..97814302,8	MCF-7	breast:
5	chr16:28832667..28835339-chr9:97766191..97767859,2	MCF-7	breast:
6	chr6:57036948..57037917-chr9:97766420..97767200,2	Hela-S3	cervix:
7	chr9:97674991..97691307-chr9:97751911..97773298,151	MCF-7	breast:
8	chr17:62222763..62223518-chr9:97766146..97766865,2	Hela-S3	cervix:
9	chr9:97763635..97773461-chr9:97847821..97861280,36	MCF-7	breast:

Variant related genes	Relation type
C9orf3	TF binding region
ENSG00000231806	Chromatin interaction
ENSG00000168488	Chromatin interaction
ENSG00000207617	Chromatin interaction
ENSG00000148120	Chromatin interaction
ENSG00000226803	Chromatin interaction
ENSG00000260796	Chromatin interaction
ENSG00000199753	Chromatin interaction
ENSG00000112208	Chromatin interaction
ENSG00000266402	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

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	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	esv3393598	chr9:97765956-97768504	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
3	esv3399008	chr9:97766206-97768629	Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97765000-97768600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr9:97765000-97770400	Active TSS	Rectal Mucosa Donor 31	rectum
3	chr9:97765200-97770600	Active TSS	Aorta	Aorta
4	chr9:97765400-97767800	Active TSS	HSMM	muscle
5	chr9:97765800-97767000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr9:97765800-97767800	Active TSS	Liver	Liver
7	chr9:97765800-97767800	Active TSS	A549	lung
8	chr9:97765800-97770800	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr9:97765800-97772600	Active TSS	Stomach Smooth Muscle	stomach
10	chr9:97766000-97766600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr9:97766000-97766600	Flanking Active TSS	HUVEC	blood vessel
12	chr9:97766000-97766800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
13	chr9:97766000-97766800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr9:97766000-97768200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
15	chr9:97766000-97768600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:97766000-97768800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:97766000-97769000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
18	chr9:97766000-97769000	Active TSS	GM12878-XiMat	blood
19	chr9:97766000-97770000	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr9:97766000-97770200	Active TSS	Duodenum Mucosa	Duodenum
21	chr9:97766000-97770400	Active TSS	Ovary	ovary
22	chr9:97766000-97770400	Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr9:97766000-97770400	Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr9:97766000-97770400	Active TSS	NHLF	lung
25	chr9:97766000-97770600	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr9:97766000-97770600	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr9:97766000-97770800	Active TSS	Colonic Mucosa	Colon
28	chr9:97766000-97771000	Active TSS	Colon Smooth Muscle	Colon
29	chr9:97766200-97766600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
30	chr9:97766200-97766600	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
31	chr9:97766200-97766600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
32	chr9:97766200-97766600	Flanking Active TSS	Brain Anterior Caudate	brain
33	chr9:97766200-97766600	Flanking Active TSS	K562	blood
34	chr9:97766200-97766800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr9:97766200-97766800	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr9:97766200-97766800	Active TSS	Stomach Mucosa	stomach
37	chr9:97766200-97766800	Flanking Active TSS	HMEC	breast
38	chr9:97766200-97767000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr9:97766200-97767000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
40	chr9:97766200-97767400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr9:97766200-97767600	Active TSS	Muscle Satellite Cultured Cells	--
42	chr9:97766200-97767800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr9:97766200-97768000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
44	chr9:97766200-97768200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr9:97766200-97768400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
46	chr9:97766200-97768800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr9:97766200-97768800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr9:97766200-97769000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr9:97766200-97769400	Active TSS	Placenta	Placenta
50	chr9:97766200-97770400	Active TSS	Left Ventricle	heart

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