Variant report

Variant	rs11789254
Chromosome Location	chr9:117459210-117459211
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	EBF1	chr9:117458832-117459908	GM12878	blood:	n/a	chr9:117459141-117459152
2	BATF	chr9:117458938-117459917	GM12878	blood:	n/a	n/a
3	MXI1	chr9:117459039-117459780	GM12878	blood:	n/a	chr9:117459441-117459450
4	FOXM1	chr9:117458886-117459923	GM12878	blood:	n/a	n/a
5	BHLHE40	chr9:117459044-117459846	GM12878	blood:	n/a	n/a
6	NFATC1	chr9:117458943-117459889	GM12878	blood:	n/a	n/a
7	TCF3	chr9:117459054-117459408	GM12878	blood:	n/a	n/a
8	RUNX3	chr9:117458873-117460027	GM12878	blood:	n/a	n/a
9	POU2F2	chr9:117458965-117459475	GM12891	blood:	n/a	chr9:117459433-117459445
10	EBF1	chr9:117458832-117459749	GM12878	blood:	n/a	chr9:117459141-117459152
11	IRF4	chr9:117458937-117459991	GM12878	blood:	n/a	n/a
12	RCOR1	chr9:117459021-117459925	GM12878	blood:	n/a	n/a
13	MEF2A	chr9:117458887-117459891	GM12878	blood:	n/a	n/a
14	BCLAF1	chr9:117458957-117460035	GM12878	blood:	n/a	chr9:117459654-117459663 chr9:117459655-117459664
15	ZEB1	chr9:117459093-117459596	GM12878	blood:	n/a	n/a
16	WRNIP1	chr9:117459130-117459308	GM12878	blood:	n/a	n/a
17	PAX5	chr9:117459063-117459434	GM12878	blood:	n/a	n/a
18	CHD2	chr9:117459003-117459926	GM12878	blood:	n/a	n/a
19	NFIC	chr9:117458759-117460117	GM12878	blood:	n/a	n/a
20	SP1	chr9:117458872-117459442	GM12878	blood:	n/a	chr9:117459288-117459300 chr9:117459288-117459300 chr9:117459289-117459298
21	RELA	chr9:117459054-117459877	GM15510	blood:	n/a	n/a
22	MEF2C	chr9:117458931-117459985	GM12878	blood:	n/a	n/a
23	BATF	chr9:117458835-117459922	GM12878	blood:	n/a	n/a
24	POU2F2	chr9:117458904-117459918	GM12891	blood:	n/a	chr9:117459433-117459445
25	BCL3	chr9:117458978-117459390	GM12878	blood:	n/a	n/a
26	SMC3	chr9:117459019-117459263	GM12878	blood:	n/a	n/a
27	RELA	chr9:117459078-117460055	GM19099	blood:	n/a	n/a
28	RELA	chr9:117459017-117459866	GM19193	blood:	n/a	n/a
29	RELA	chr9:117459066-117459796	GM10847	blood:	n/a	n/a
30	JUND	chr9:117459141-117460073	SK-N-SH	brain:	n/a	chr9:117459655-117459664 chr9:117459656-117459667 chr9:117459655-117459662 chr9:117459655-117459663 chr9:117459653-117459664 chr9:117459654-117459663
31	YY1	chr9:117459168-117459555	GM12892	blood:	n/a	n/a
32	STAT5A	chr9:117458963-117459880	GM12878	blood:	n/a	chr9:117459654-117459663 chr9:117459655-117459664
33	NFIC	chr9:117458791-117459937	GM12878	blood:	n/a	n/a
34	YY1	chr9:117459001-117459500	GM12878	blood:	n/a	n/a
35	MTA3	chr9:117458852-117459422	GM12878	blood:	n/a	n/a
36	POU2F2	chr9:117458918-117459916	GM12878	blood:	n/a	chr9:117459433-117459445
37	ATF2	chr9:117458851-117459964	GM12878	blood:	n/a	n/a
38	YY1	chr9:117459043-117459460	GM12892	blood:	n/a	n/a
39	PAX5	chr9:117458866-117459961	GM12878	blood:	n/a	chr9:117459549-117459558
40	CEBPB	chr9:117459069-117459428	GM12878	blood:	n/a	n/a
41	BCL11A	chr9:117458914-117459921	GM12878	blood:	n/a	chr9:117459654-117459663 chr9:117459655-117459664
42	PAX5	chr9:117459038-117459401	GM12878	blood:	n/a	n/a
43	TCF3	chr9:117459001-117459485	GM12878	blood:	n/a	chr9:117459441-117459454
44	ATF2	chr9:117458844-117459975	GM12878	blood:	n/a	n/a
45	EP300	chr9:117458993-117459445	GM12878	blood:	n/a	n/a
46	MTA3	chr9:117458874-117460796	GM12878	blood:	n/a	n/a
47	CEBPB	chr9:117458818-117460003	GM12878	blood:	n/a	n/a
48	STAT3	chr9:117458981-117459918	GM12878	blood:	n/a	chr9:117459654-117459663 chr9:117459655-117459664
49	NFATC1	chr9:117458957-117459893	GM12878	blood:	n/a	n/a
50	YY1	chr9:117459087-117459662	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000230284	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11788301	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11788303	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11789913	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11790078	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11791529	1.00[ASN][1000 genomes]
rs11793039	1.00[ASN][1000 genomes]
rs11793592	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11793719	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11793753	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11794319	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11794322	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16930795	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16930910	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16930928	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17235713	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2031877	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28420964	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41278671	0.81[EUR][1000 genomes]
rs56357980	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044374	chr9:116955841-117460150	Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
2	nsv831694	chr9:117328640-117502785	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv893766	chr9:117385992-117516418	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1042718	chr9:117435306-117488969	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117454200-117459600	Weak transcription	Hela-S3	cervix
2	chr9:117456200-117460000	Weak transcription	Small Intestine	intestine
3	chr9:117457400-117459600	Weak transcription	HSMMtube	muscle
4	chr9:117457600-117459400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:117457600-117459400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr9:117457600-117459400	Weak transcription	HMEC	breast
7	chr9:117457600-117459600	Weak transcription	NH-A	brain
8	chr9:117457600-117459800	Enhancers	GM12878-XiMat	blood
9	chr9:117457600-117462200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr9:117458800-117460200	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr9:117458800-117460400	Enhancers	Primary T cells fromperipheralblood	blood
12	chr9:117458800-117460400	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr9:117458800-117460600	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr9:117458800-117461000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr9:117459000-117459800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr9:117459000-117459800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr9:117459000-117459800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr9:117459000-117459800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr9:117459000-117460000	Enhancers	HSMM	muscle
20	chr9:117459000-117460200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr9:117459000-117460200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr9:117459000-117460200	Enhancers	NHDF-Ad	bronchial
23	chr9:117459000-117460400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr9:117459000-117461000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr9:117459200-117459600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr9:117459200-117459600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr9:117459200-117459800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr9:117459200-117459800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:117459200-117460000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:117459200-117460000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr9:117459200-117460000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr9:117459200-117460000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr9:117459200-117460000	Enhancers	NHEK	skin
34	chr9:117459200-117460000	Enhancers	NHLF	lung
35	chr9:117459200-117460000	Enhancers	Osteobl	bone
36	chr9:117459200-117460400	Enhancers	Primary T helper naive cells from peripheral blood	blood

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