Variant report

Variant	rs12337200
Chromosome Location	chr9:116036721-116036722
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	CTCF	chr9:116036702-116037076	A549	lung:	n/a	n/a
2	POLR2A	chr9:116036438-116039178	MCF10A-Er-Src	breast:	n/a	n/a
3	IRF1	chr9:116036651-116038361	K562	blood:	n/a	n/a
4	CTCF	chr9:116036026-116037453	A549	lung:	n/a	n/a
5	RAD21	chr9:116036697-116037049	GM12878	blood:	n/a	n/a
6	EBF1	chr9:116036720-116036935	GM12878	blood:	n/a	n/a
7	SIN3AK20	chr9:116036628-116038581	MCF-7	breast:	n/a	n/a
8	SMC3	chr9:116036709-116037054	HepG2	liver:	n/a	n/a
9	CTCF	chr9:116036707-116037005	SK-N-SH_RA	brain:	n/a	n/a
10	POLR2A	chr9:116036665-116039023	MCF10A-Er-Src	breast:	n/a	n/a
11	CTCF	chr9:116036585-116037165	MCF-7	breast:	n/a	n/a
12	CTCF	chr9:116036716-116037046	GM12878	blood:	n/a	n/a
13	POLR2A	chr9:116036286-116038980	GM12891	blood:	n/a	n/a
14	ZNF143	chr9:116036487-116038353	K562	blood:	n/a	chr9:116037848-116037866 chr9:116037852-116037871 chr9:116037344-116037354
15	RAD21	chr9:116036572-116037175	HepG2	liver:	n/a	n/a
16	NR2F2	chr9:116036676-116037301	K562	blood:	n/a	chr9:116036909-116036924
17	CHD1	chr9:116035600-116039131	IMR90	lung:	n/a	n/a
18	RCOR1	chr9:116036684-116038442	Hela-S3	cervix:	n/a	n/a
19	SMC3	chr9:116036637-116037474	GM12878	blood:	n/a	n/a
20	MYC	chr9:116036688-116037118	MCF10A-Er-Src	breast:	n/a	n/a
21	RAD21	chr9:116036681-116037092	HepG2	liver:	n/a	n/a
22	EP300	chr9:116036616-116038189	K562	blood:	n/a	chr9:116038069-116038085 chr9:116037457-116037464 chr9:116037975-116037988
23	RAD21	chr9:116036653-116037134	Hela-S3	cervix:	n/a	n/a
24	TBP	chr9:116036601-116038597	Hela-S3	cervix:	n/a	n/a
25	RAD21	chr9:116036583-116037169	HCT-116	colon:	n/a	n/a
26	RCOR1	chr9:116036689-116037300	GM12878	blood:	n/a	n/a
27	BRCA1	chr9:116036695-116037024	H1-hESC	embryonic stem cell:	n/a	n/a
28	RFX5	chr9:116036671-116038237	Hela-S3	cervix:	n/a	chr9:116037527-116037542 chr9:116037527-116037542 chr9:116037527-116037542 chr9:116037526-116037543
29	RAD21	chr9:116036238-116039041	SK-N-SH	brain:	n/a	chr9:116037583-116037595 chr9:116038010-116038023
30	MYC	chr9:116036669-116038515	K562	blood:	n/a	chr9:116037899-116037908
31	ZNF143	chr9:116036699-116038204	GM12878	blood:	n/a	chr9:116037848-116037866 chr9:116037852-116037871 chr9:116037344-116037354
32	CTCF	chr9:116036666-116037078	A549	lung:	n/a	n/a
33	CTCF	chr9:116036700-116036850	NHEK	skin:	n/a	n/a
34	CTCF	chr9:116036675-116037149	MCF-7	breast:	n/a	n/a
35	SIN3A	chr9:116036705-116038652	H1-hESC	embryonic stem cell:	n/a	n/a
36	NR2F2	chr9:116036668-116037219	MCF-7	breast:	n/a	chr9:116036909-116036924
37	RAD21	chr9:116036573-116037103	MCF-7	breast:	n/a	n/a
38	POLR2A	chr9:116036665-116038914	K562	blood:	n/a	n/a
39	RAD21	chr9:116036704-116037058	HepG2	liver:	n/a	n/a
40	HNF4G	chr9:116036719-116037030	HepG2	liver:	n/a	chr9:116036764-116036777 chr9:116036909-116036924 chr9:116036764-116036777
41	RAD21	chr9:116036697-116036955	GM12878	blood:	n/a	n/a
42	CTCF	chr9:116036700-116036850	GM12878	blood:	n/a	n/a
43	CTCF	chr9:116036720-116036870	HAc	cerebellar:	n/a	n/a
44	RAD21	chr9:116036711-116037168	K562	blood:	n/a	n/a
45	TBP	chr9:116036626-116038497	GM12878	blood:	n/a	n/a
46	ZNF384	chr9:116036689-116037117	K562	blood:	n/a	n/a
47	MXI1	chr9:116036564-116038986	SK-N-SH	brain:	n/a	chr9:116037526-116037541 chr9:116037528-116037543
48	MTA3	chr9:116036610-116038487	GM12878	blood:	n/a	n/a
49	ZNF384	chr9:116036660-116037078	GM12878	blood:	n/a	n/a
50	CHD1	chr9:116036634-116038375	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:116035093..116036761-chr9:116347708..116350133,2	K562	blood:
2	chr9:116035655..116037372-chr9:116289546..116291507,2	K562	blood:
3	chr9:116036437..116039850-chr9:116170281..116174782,6	K562	blood:
4	chr9:115981728..115986983-chr9:116035777..116040437,9	K562	blood:
5	chr9:115875131..115875649-chr9:116036597..116037161,2	MCF-7	breast:
6	chr9:116035556..116040148-chr9:116171147..116174619,7	K562	blood:
7	chr9:116036423..116037332-chr9:116419975..116420491,2	K562	blood:
8	chr9:116036612..116039217-chr9:116063138..116067985,4	MCF-7	breast:
9	chr9:116036369..116037533-chr9:116417343..116418092,4	K562	blood:
10	chr9:116036323..116039598-chr9:116161482..116165034,3	MCF-7	breast:
11	chr9:116033413..116040476-chr9:116169994..116174441,15	MCF-7	breast:
12	chr9:116036224..116039468-chr9:116162090..116165920,4	MCF-7	breast:
13	chr9:116035030..116037849-chr9:116344314..116346129,2	K562	blood:
14	chr9:115982263..115984734-chr9:116036359..116038354,4	MCF-7	breast:
15	chr9:116036482..116037335-chr9:116168680..116169652,2	MCF-7	breast:
16	chr9:115982005..115986983-chr9:116035777..116039702,5	K562	blood:
17	chr9:116036349..116038748-chr9:116343941..116345814,2	K562	blood:
18	chr9:116035986..116039204-chr9:116098421..116104240,5	MCF-7	breast:
19	chr9:115983488..115985496-chr9:116035418..116038927,3	MCF-7	breast:
20	chr9:116035314..116038256-chr9:116326581..116329349,2	K562	blood:
21	chr9:116036149..116038435-chr9:116101107..116104521,3	K562	blood:

Variant related genes	Relation type
PRPF4	TF binding region
ENSG00000165188	Chromatin interaction
ENSG00000157653	Chromatin interaction
ENSG00000148225	Chromatin interaction
ENSG00000119321	Chromatin interaction
ENSG00000136868	Chromatin interaction
ENSG00000231528	Chromatin interaction
ENSG00000138835	Chromatin interaction
ENSG00000148229	Chromatin interaction
ENSG00000148218	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10117320	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16931988	1.00[EUR][1000 genomes]
rs73552275	1.00[EUR][1000 genomes]
rs7858004	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116008200-116037000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:116023000-116036800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:116033800-116036800	Weak transcription	Psoas Muscle	Psoas
4	chr9:116034400-116037000	Weak transcription	Small Intestine	intestine
5	chr9:116035200-116036800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr9:116035200-116036800	Weak transcription	Aorta	Aorta
7	chr9:116035200-116036800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr9:116035200-116036800	Weak transcription	Right Ventricle	heart
9	chr9:116035200-116036800	Weak transcription	Thymus	Thymus
10	chr9:116035200-116037000	Weak transcription	Lung	lung
11	chr9:116035200-116037000	Weak transcription	Ovary	ovary
12	chr9:116035200-116037200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr9:116035400-116036800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr9:116035400-116036800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr9:116035400-116036800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr9:116035400-116037000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:116035400-116037000	Weak transcription	Left Ventricle	heart
18	chr9:116035400-116037000	Weak transcription	Pancreas	Pancrea
19	chr9:116035400-116037200	Weak transcription	Spleen	Spleen
20	chr9:116035800-116036800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr9:116035800-116036800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr9:116035800-116036800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr9:116035800-116036800	Weak transcription	Colonic Mucosa	Colon
24	chr9:116035800-116036800	Weak transcription	Fetal Thymus	thymus
25	chr9:116035800-116037000	Weak transcription	Gastric	stomach
26	chr9:116036000-116036800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr9:116036000-116036800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr9:116036000-116036800	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr9:116036000-116036800	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr9:116036000-116036800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr9:116036000-116036800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr9:116036000-116036800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr9:116036000-116036800	Weak transcription	Fetal Muscle Leg	muscle
34	chr9:116036000-116037000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:116036000-116037000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr9:116036000-116037000	Weak transcription	Esophagus	oesophagus
37	chr9:116036000-116037000	Weak transcription	Placenta	Placenta
38	chr9:116036000-116037000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr9:116036200-116036800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr9:116036200-116036800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr9:116036200-116036800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr9:116036200-116036800	Enhancers	Hela-S3	cervix
43	chr9:116036400-116036800	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr9:116036400-116036800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr9:116036400-116036800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr9:116036400-116036800	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr9:116036400-116036800	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr9:116036400-116036800	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr9:116036400-116036800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr9:116036400-116036800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links