Variant report

Variant	rs28581753
Chromosome Location	chr9:26893521-26893522
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:26891697-26893623	Raji	blood:	n/a	n/a
2	POLR2A	chr9:26891986-26893579	K562	blood:	n/a	n/a
3	POLR2A	chr9:26891461-26893661	GM19099	blood:	n/a	n/a
4	MAFK	chr9:26892251-26893559	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr9:26891959-26893696	HepG2	liver:	n/a	n/a
6	POLR2A	chr9:26892149-26893642	GM12878	blood:	n/a	n/a
7	CHD1	chr9:26892031-26893555	GM12878	blood:	n/a	n/a
8	TBL1XR1	chr9:26893140-26893586	K562	blood:	n/a	n/a
9	POLR2A	chr9:26891662-26893570	GM18505	blood:	n/a	n/a
10	POLR2A	chr9:26891212-26893831	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr9:26890917-26893711	K562	blood:	n/a	n/a
12	POLR2A	chr9:26891580-26893690	K562	blood:	n/a	n/a
13	TBL1XR1	chr9:26891049-26893676	K562	blood:	n/a	n/a
14	POLR2A	chr9:26891781-26893654	PBDE	blood:	n/a	n/a
15	ZNF143	chr9:26892002-26893542	K562	blood:	n/a	n/a
16	POLR2A	chr9:26891475-26893753	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr9:26891084-26893746	MCF10A-Er-Src	breast:	n/a	n/a
18	HCFC1	chr9:26891245-26893651	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr9:26891262-26893632	IMR90	lung:	n/a	n/a
20	POLR2A	chr9:26892219-26893612	A549	lung:	n/a	n/a
21	POLR2A	chr9:26891608-26893599	Hela-S3	cervix:	n/a	n/a
22	WRNIP1	chr9:26892049-26893622	GM12878	blood:	n/a	n/a
23	POLR2A	chr9:26893119-26893714	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr9:26892057-26893624	K562	blood:	n/a	n/a
25	POLR2A	chr9:26891406-26893775	GM12891	blood:	n/a	n/a
26	POLR2A	chr9:26891979-26893784	SK-N-MC	brain:	n/a	n/a
27	SMC3	chr9:26893465-26893592	GM12878	blood:	n/a	n/a
28	POLR2A	chr9:26891503-26893712	GM12878	blood:	n/a	n/a
29	POLR2A	chr9:26891564-26893564	HepG2	liver:	n/a	n/a
30	POLR2A	chr9:26891463-26893612	Hela-S3	cervix:	n/a	n/a
31	MXI1	chr9:26890843-26893800	SK-N-SH	brain:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:26891080..26895841-chr9:26945501..26948974,8	K562	blood:
2	chr9:26891080..26894676-chr9:26945695..26949113,9	K562	blood:
3	chr9:26891289..26894164-chr9:26921199..26924471,3	MCF-7	breast:
4	chr9:26890425..26894629-chr9:26953159..26958312,6	K562	blood:
5	chr9:26891902..26893962-chr9:26955453..26958235,3	MCF-7	breast:
6	chr9:26892381..26894407-chr9:26894414..26897617,3	MCF-7	breast:
7	chr9:26891939..26894308-chr9:26895080..26897868,2	K562	blood:
8	chr9:26890972..26893985-chr9:26945405..26948624,3	MCF-7	breast:
9	chr9:26892948..26894662-chr9:26974221..26975842,2	K562	blood:
10	chr9:26889862..26894629-chr9:26953159..26958871,9	K562	blood:

No data

Variant related genes	Relation type
RN7SL100P	TF binding region
CAAP1	TF binding region
ENSG00000240306	Chromatin interaction
ENSG00000096872	Chromatin interaction
ENSG00000137055	Chromatin interaction
ENSG00000234676	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10967605	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12000190	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12000194	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12000403	0.91[EUR][1000 genomes]
rs12000745	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12000936	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12002016	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12002242	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12002247	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12002844	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12002995	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12003566	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12004175	0.91[EUR][1000 genomes]
rs12005788	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12005943	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12005959	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16910907	0.91[EUR][1000 genomes]
rs16910929	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41271179	0.91[EUR][1000 genomes]
rs59452957	0.91[EUR][1000 genomes]
rs60097289	0.91[EUR][1000 genomes]
rs7043002	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73643108	0.91[EUR][1000 genomes]
rs73643115	0.84[EUR][1000 genomes]
rs73643116	0.88[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026827	chr9:26693515-26904699	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26888200-26893600	Active TSS	K562	blood
2	chr9:26890200-26893600	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr9:26890400-26894400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr9:26890600-26893600	Active TSS	Fetal Intestine Small	intestine
5	chr9:26890600-26893600	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr9:26890800-26893600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:26890800-26893600	Active TSS	HSMM	muscle
8	chr9:26891000-26893600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:26891200-26893600	Active TSS	Brain Anterior Caudate	brain
10	chr9:26891200-26893600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr9:26891400-26893600	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr9:26891400-26893600	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr9:26891400-26893600	Bivalent/Poised TSS	HepG2	liver
14	chr9:26891600-26893600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr9:26891800-26893600	Active TSS	Brain Germinal Matrix	brain
16	chr9:26891800-26893600	Active TSS	Rectal Smooth Muscle	rectum
17	chr9:26891800-26893600	Active TSS	Stomach Smooth Muscle	stomach
18	chr9:26892000-26893600	Active TSS	Monocytes-CD14+_RO01746	blood
19	chr9:26892600-26893600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr9:26892800-26916200	Weak transcription	Small Intestine	intestine
21	chr9:26893000-26893600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr9:26893000-26893600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr9:26893000-26893600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr9:26893000-26893600	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr9:26893000-26893600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr9:26893000-26893600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr9:26893000-26893600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr9:26893000-26893600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr9:26893000-26893600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr9:26893000-26893600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr9:26893000-26893600	Flanking Active TSS	Liver	Liver
32	chr9:26893000-26893600	Flanking Active TSS	Fetal Kidney	kidney
33	chr9:26893000-26893600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr9:26893000-26893600	Flanking Active TSS	Dnd41	blood
35	chr9:26893000-26893600	Flanking Active TSS	GM12878-XiMat	blood
36	chr9:26893000-26893600	Flanking Active TSS	Hela-S3	cervix
37	chr9:26893000-26893600	Flanking Active TSS	HMEC	breast
38	chr9:26893000-26893600	Flanking Active TSS	NHEK	skin
39	chr9:26893000-26893600	Flanking Active TSS	NHLF	lung
40	chr9:26893000-26893600	Flanking Active TSS	Osteobl	bone
41	chr9:26893000-26905600	Weak transcription	Lung	lung
42	chr9:26893000-26916000	Weak transcription	Left Ventricle	heart
43	chr9:26893000-26916000	Weak transcription	Pancreas	Pancrea
44	chr9:26893000-26916200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:26893000-26922600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr9:26893000-26924200	Weak transcription	Esophagus	oesophagus
47	chr9:26893200-26893600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr9:26893200-26893600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr9:26893200-26893600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr9:26893200-26893600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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