Variant report

Variant	rs12339708
Chromosome Location	chr9:26954377-26954378
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr9:26953990-26955652	U2OS	brain:	n/a	n/a
2	CTCF	chr9:26954121-26954611	K562	blood:	n/a	n/a
3	STAT1	chr9:26953941-26954454	K562	blood:	n/a	n/a
4	EP300	chr9:26954078-26954747	K562	blood:	n/a	n/a
5	POLR2A	chr9:26953691-26954849	GM12892	blood:	n/a	n/a
6	POLR2A	chr9:26953902-26957243	PBDE	blood:	n/a	n/a
7	TBP	chr9:26954173-26954561	GM12878	blood:	n/a	n/a
8	CTCF	chr9:26954320-26954470	RPTEC	kidney:	n/a	n/a
9	CTCF	chr9:26954340-26954490	NB4	blood:	n/a	n/a
10	CTCF	chr9:26954360-26954510	GM12878	blood:	n/a	n/a
11	RCOR1	chr9:26953922-26954491	GM12878	blood:	n/a	n/a
12	ELK1	chr9:26954162-26954388	GM12878	blood:	n/a	n/a
13	SRF	chr9:26954177-26954520	GM12878	blood:	n/a	chr9:26954328-26954346
14	SRF	chr9:26954223-26954476	K562	blood:	n/a	chr9:26954328-26954346
15	NRF1	chr9:26954239-26954535	GM12878	blood:	n/a	n/a
16	CTCF	chr9:26954360-26954510	HL-60	blood:	n/a	n/a
17	IRF1	chr9:26954004-26954928	K562	blood:	n/a	n/a
18	CTCF	chr9:26954360-26954510	HPAF	blood vessel:	n/a	n/a
19	CTCF	chr9:26954300-26954450	HMF	breast:	n/a	n/a
20	STAT3	chr9:26954280-26954512	MCF10A-Er-Src	breast:	n/a	n/a
21	IRF1	chr9:26954038-26954637	K562	blood:	n/a	n/a
22	ATF1	chr9:26954089-26954498	K562	blood:	n/a	n/a
23	SETDB1	chr9:26953957-26954679	U2OS	brain:	n/a	n/a
24	SRF	chr9:26954255-26954421	HepG2	liver:	n/a	chr9:26954328-26954346
25	RCOR1	chr9:26953881-26954421	K562	blood:	n/a	n/a
26	STAT2	chr9:26953993-26954560	K562	blood:	n/a	chr9:26954253-26954268
27	CTCF	chr9:26954275-26954600	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:26890425..26894629-chr9:26953159..26958312,6	K562	blood:
2	chr9:26889862..26894629-chr9:26953159..26958871,9	K562	blood:
3	chr9:26943098..26949574-chr9:26949927..26957421,13	K562	blood:
4	chr9:26949977..26952390-chr9:26952885..26955695,2	MCF-7	breast:

No data

Variant related genes	Relation type
IFT74	TF binding region
ENSG00000096872	Chromatin interaction
ENSG00000120159	Chromatin interaction
ENSG00000137055	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10217666	1.00[AFR][1000 genomes]
rs10967618	0.91[AFR][1000 genomes]
rs10967619	0.84[AFR][1000 genomes]
rs10967620	0.84[AFR][1000 genomes]
rs10967659	1.00[AFR][1000 genomes]
rs12336174	1.00[AFR][1000 genomes]
rs12336185	1.00[AFR][1000 genomes]
rs12336232	1.00[AFR][1000 genomes]
rs12339549	0.91[AFR][1000 genomes]
rs12340112	1.00[AFR][1000 genomes]
rs12341712	1.00[AFR][1000 genomes]
rs12344880	0.82[AFR][1000 genomes]
rs12346926	1.00[AFR][1000 genomes]
rs12348593	1.00[AFR][1000 genomes]
rs12348715	0.91[AFR][1000 genomes]
rs12351839	0.91[AFR][1000 genomes]
rs12352013	0.91[AFR][1000 genomes]
rs12352278	0.91[AFR][1000 genomes]
rs13440285	1.00[AFR][1000 genomes]
rs28509785	0.91[AFR][1000 genomes]
rs28525632	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528614	chr9:26893662-27074233	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv517269	chr9:26945976-27137242	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26947600-26955200	Weak transcription	Spleen	Spleen
2	chr9:26948000-26955200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr9:26948200-26955000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr9:26948200-26955000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr9:26948200-26955000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:26948200-26955000	Weak transcription	Adipose Nuclei	Adipose
7	chr9:26948200-26955000	Weak transcription	Brain Angular Gyrus	brain
8	chr9:26948200-26955000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr9:26948200-26955000	Weak transcription	Brain Substantia Nigra	brain
10	chr9:26948200-26955000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr9:26948200-26955000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr9:26948200-26955000	Weak transcription	NHDF-Ad	bronchial
13	chr9:26948200-26955000	Weak transcription	NHLF	lung
14	chr9:26948200-26955200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr9:26948200-26955200	Weak transcription	Brain Hippocampus Middle	brain
16	chr9:26948200-26955400	Weak transcription	Psoas Muscle	Psoas
17	chr9:26948200-26955800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:26948400-26954600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr9:26948400-26955000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr9:26948400-26955200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr9:26948400-26955200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr9:26948400-26955200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr9:26948400-26955200	Weak transcription	Liver	Liver
24	chr9:26949800-26954800	Weak transcription	A549	lung
25	chr9:26949800-26955200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr9:26949800-26955400	Weak transcription	NH-A	brain
27	chr9:26950000-26955200	Weak transcription	HMEC	breast
28	chr9:26950000-26955200	Weak transcription	NHEK	skin
29	chr9:26950600-26955200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr9:26950600-26955400	Weak transcription	Hela-S3	cervix
31	chr9:26953800-26954400	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr9:26953800-26955400	Enhancers	Small Intestine	intestine
33	chr9:26953800-26956000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr9:26954000-26954400	Active TSS	Osteobl	bone
35	chr9:26954000-26954600	Active TSS	K562	blood
36	chr9:26954000-26954800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr9:26954000-26955000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr9:26954000-26955000	Enhancers	HepG2	liver
39	chr9:26954200-26954400	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr9:26954200-26955200	Enhancers	Primary hematopoietic stem cells	blood

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