Variant report

Variant	rs570899465
Chromosome Location	chr9:97766935-97766936
allele	G/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	ZBTB7A	chr9:97766636-97767007	K562	blood:	n/a	n/a
3	POLR2A	chr9:97766704-97767013	H1-neurons	neurons:	n/a	n/a
4	SIN3AK20	chr9:97766218-97767008	MCF-7	breast:	n/a	n/a
5	SIN3AK20	chr9:97766440-97766967	A549	lung:	n/a	n/a
6	SMC3	chr9:97766199-97766991	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr9:97766762-97766961	HCT-116	colon:	n/a	n/a
8	MAX	chr9:97766258-97767040	SK-N-SH	brain:	n/a	n/a
9	ELF1	chr9:97766705-97766966	K562	blood:	n/a	chr9:97766954-97766963
10	RAD21	chr9:97766289-97767005	SK-N-SH_RA	brain:	n/a	chr9:97766704-97766714
11	EP300	chr9:97766155-97767085	ECC-1	luminal epithelium:	n/a	chr9:97766680-97766696
12	UBTF	chr9:97766237-97767980	K562	blood:	n/a	n/a
13	E2F6	chr9:97766619-97767006	K562	blood:	n/a	chr9:97766836-97766843 chr9:97766836-97766843 chr9:97766903-97766915 chr9:97766836-97766843
14	MYC	chr9:97766335-97766979	K562	blood:	n/a	n/a
15	RAD21	chr9:97766218-97766997	MCF-7	breast:	n/a	chr9:97766704-97766714
16	POLR2A	chr9:97766117-97768000	ProgFib	skin:	n/a	n/a
17	POLR2A	chr9:97766619-97767603	HUVEC	blood vessel:	n/a	n/a
18	TBP	chr9:97766342-97767174	HepG2	liver:	n/a	n/a
19	MAX	chr9:97766261-97767827	HepG2	liver:	n/a	chr9:97767735-97767745
20	POLR2A	chr9:97766405-97767000	HCT-116	colon:	n/a	n/a
21	RFX5	chr9:97766088-97766987	HepG2	liver:	n/a	n/a
22	TAF1	chr9:97766616-97767807	HepG2	liver:	n/a	n/a
23	HEY1	chr9:97766234-97766996	HepG2	liver:	n/a	chr9:97766677-97766692 chr9:97766679-97766694
24	RAD21	chr9:97766342-97766984	H1-hESC	embryonic stem cell:	n/a	chr9:97766704-97766714
25	POLR2A	chr9:97765950-97767012	HUVEC	blood vessel:	n/a	n/a
26	EGR1	chr9:97766906-97767241	ECC-1	luminal epithelium:	n/a	chr9:97767161-97767171
27	POLR2A	chr9:97766071-97767003	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr9:97766618-97766987	GM12878	blood:	n/a	n/a
29	RAD21	chr9:97766723-97767036	HepG2	liver:	n/a	n/a
30	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
31	SP1	chr9:97765773-97767001	A549	lung:	n/a	chr9:97766690-97766699
32	MAZ	chr9:97766396-97766984	Hela-S3	cervix:	n/a	n/a
33	MTA3	chr9:97766618-97766976	GM12878	blood:	n/a	n/a
34	POLR2A	chr9:97765858-97769286	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr9:97766333-97767062	HepG2	liver:	n/a	n/a
36	RFX5	chr9:97764166-97767012	SK-N-SH	brain:	n/a	chr9:97764370-97764385 chr9:97764370-97764385
37	EP300	chr9:97766711-97767112	HepG2	liver:	n/a	n/a
38	POLR2A	chr9:97766419-97767795	MCF-7	breast:	n/a	n/a
39	TBP	chr9:97766284-97767606	K562	blood:	n/a	n/a
40	POLR2A	chr9:97766436-97767044	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr9:97766292-97767194	PANC-1	pancreas:	n/a	n/a
42	EGR1	chr9:97766758-97767225	K562	blood:	n/a	chr9:97767161-97767171
43	MAZ	chr9:97766333-97767713	K562	blood:	n/a	n/a
44	REST	chr9:97765810-97767007	A549	lung:	n/a	n/a
45	POLR2A	chr9:97766051-97769186	MCF10A-Er-Src	breast:	n/a	n/a
46	MAX	chr9:97766393-97767016	MCF-7	breast:	n/a	n/a
47	POLR2A	chr9:97766777-97766946	K562	blood:	n/a	n/a
48	RAD21	chr9:97766207-97767036	IMR90	lung:	n/a	chr9:97766704-97766714
49	MAX	chr9:97766190-97767372	A549	lung:	n/a	n/a
50	CEBPD	chr9:97766700-97767114	HepG2	liver:	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	chr9:97763635..97773461-chr9:97847821..97861280,36	MCF-7	breast:

Variant related genes	Relation type
C9orf3	TF binding region
ENSG00000260796	Chromatin interaction
ENSG00000207617	Chromatin interaction
ENSG00000112208	Chromatin interaction
ENSG00000231806	Chromatin interaction
ENSG00000168488	Chromatin interaction
ENSG00000148120	Chromatin interaction
ENSG00000226803	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:123 , 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	chr9:97766000-97768200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr9:97766000-97768600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:97766000-97768800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:97766000-97769000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
14	chr9:97766000-97769000	Active TSS	GM12878-XiMat	blood
15	chr9:97766000-97770000	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr9:97766000-97770200	Active TSS	Duodenum Mucosa	Duodenum
17	chr9:97766000-97770400	Active TSS	Ovary	ovary
18	chr9:97766000-97770400	Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr9:97766000-97770400	Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr9:97766000-97770400	Active TSS	NHLF	lung
21	chr9:97766000-97770600	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr9:97766000-97770600	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr9:97766000-97770800	Active TSS	Colonic Mucosa	Colon
24	chr9:97766000-97771000	Active TSS	Colon Smooth Muscle	Colon
25	chr9:97766200-97767000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr9:97766200-97767000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
27	chr9:97766200-97767400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr9:97766200-97767600	Active TSS	Muscle Satellite Cultured Cells	--
29	chr9:97766200-97767800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr9:97766200-97768000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
31	chr9:97766200-97768200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr9:97766200-97768400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
33	chr9:97766200-97768800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr9:97766200-97768800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr9:97766200-97769000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr9:97766200-97769400	Active TSS	Placenta	Placenta
37	chr9:97766200-97770400	Active TSS	Left Ventricle	heart
38	chr9:97766200-97770600	Active TSS	Brain Hippocampus Middle	brain
39	chr9:97766200-97771000	Active TSS	Right Ventricle	heart
40	chr9:97766200-97771200	Active TSS	Fetal Kidney	kidney
41	chr9:97766200-97771800	Active TSS	Right Atrium	heart
42	chr9:97766400-97767000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
43	chr9:97766400-97767000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
44	chr9:97766400-97767000	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
45	chr9:97766400-97767000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr9:97766400-97767000	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
47	chr9:97766400-97767000	Bivalent Enhancer	Fetal Brain Male	brain
48	chr9:97766400-97767000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
49	chr9:97766400-97767000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
50	chr9:97766400-97767000	Flanking Bivalent TSS/Enh	Thymus	Thymus

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