Variant report

Variant	rs3739546
Chromosome Location	chr9:26893323-26893324
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:55)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:55 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:26892134-26893327	PFSK-1	brain:	n/a	n/a
2	CHD1	chr9:26891432-26893429	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr9:26891907-26893486	GM12892	blood:	n/a	n/a
4	POLR2A	chr9:26891697-26893623	Raji	blood:	n/a	n/a
5	EP300	chr9:26892207-26893438	K562	blood:	n/a	chr9:26892776-26892792 chr9:26892821-26892828
6	ARID3A	chr9:26892177-26893347	K562	blood:	n/a	n/a
7	POLR2A	chr9:26891986-26893579	K562	blood:	n/a	n/a
8	POLR2A	chr9:26891461-26893661	GM19099	blood:	n/a	n/a
9	MAFK	chr9:26892251-26893559	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr9:26891959-26893696	HepG2	liver:	n/a	n/a
11	POLR2A	chr9:26892149-26893642	GM12878	blood:	n/a	n/a
12	MAX	chr9:26891979-26893383	A549	lung:	n/a	chr9:26892866-26892876
13	POLR2A	chr9:26891588-26893359	HepG2	liver:	n/a	n/a
14	PML	chr9:26891985-26893337	GM12878	blood:	n/a	n/a
15	CHD1	chr9:26892031-26893555	GM12878	blood:	n/a	n/a
16	TBL1XR1	chr9:26893140-26893586	K562	blood:	n/a	n/a
17	POLR2A	chr9:26891662-26893570	GM18505	blood:	n/a	n/a
18	POLR2A	chr9:26891212-26893831	MCF10A-Er-Src	breast:	n/a	n/a
19	CHD2	chr9:26892168-26893460	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr9:26890917-26893711	K562	blood:	n/a	n/a
21	POLR2A	chr9:26892113-26893449	K562	blood:	n/a	n/a
22	POLR2A	chr9:26891580-26893690	K562	blood:	n/a	n/a
23	ZC3H11A	chr9:26892228-26893401	K562	blood:	n/a	n/a
24	TBL1XR1	chr9:26891049-26893676	K562	blood:	n/a	n/a
25	POLR2A	chr9:26891781-26893654	PBDE	blood:	n/a	n/a
26	ZNF143	chr9:26892002-26893542	K562	blood:	n/a	n/a
27	MTA3	chr9:26892376-26893363	GM12878	blood:	n/a	n/a
28	POLR2A	chr9:26891475-26893753	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr9:26891084-26893746	MCF10A-Er-Src	breast:	n/a	n/a
30	HCFC1	chr9:26891245-26893651	Hela-S3	cervix:	n/a	n/a
31	MTA3	chr9:26892066-26893438	GM12878	blood:	n/a	n/a
32	MAZ	chr9:26892136-26893373	IMR90	lung:	n/a	chr9:26892866-26892876
33	MYC	chr9:26891817-26893352	K562	blood:	n/a	chr9:26892866-26892876
34	POLR2A	chr9:26891262-26893632	IMR90	lung:	n/a	n/a
35	POLR2A	chr9:26892147-26893445	GM18526	blood:	n/a	n/a
36	KAP1	chr9:26891492-26893419	HEK293	kidney:	n/a	n/a
37	CHD2	chr9:26892142-26893323	GM12878	blood:	n/a	n/a
38	POLR2A	chr9:26892219-26893612	A549	lung:	n/a	n/a
39	POLR2A	chr9:26891608-26893599	Hela-S3	cervix:	n/a	n/a
40	WRNIP1	chr9:26892049-26893622	GM12878	blood:	n/a	n/a
41	POLR2A	chr9:26893119-26893714	H1-hESC	embryonic stem cell:	n/a	n/a
42	GABPA	chr9:26892169-26893323	SK-N-SH	brain:	n/a	n/a
43	POLR2A	chr9:26892057-26893624	K562	blood:	n/a	n/a
44	POLR2A	chr9:26891406-26893775	GM12891	blood:	n/a	n/a
45	POLR2A	chr9:26891979-26893784	SK-N-MC	brain:	n/a	n/a
46	GABPA	chr9:26892089-26893413	MCF-7	breast:	n/a	n/a
47	POLR2A	chr9:26891503-26893712	GM12878	blood:	n/a	n/a
48	POLR2A	chr9:26891564-26893564	HepG2	liver:	n/a	n/a
49	POLR2A	chr9:26893207-26893480	GM12891	blood:	n/a	n/a
50	POLR2A	chr9:26891463-26893612	Hela-S3	cervix:	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
CAAP1	TF binding region
RN7SL100P	TF binding region
ENSG00000234676	Chromatin interaction
ENSG00000137055	Chromatin interaction
ENSG00000240306	Chromatin interaction
ENSG00000096872	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs62544453	0.80[ASN][1000 genomes]
rs73433937	0.80[ASN][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:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26888200-26893600	Active TSS	K562	blood
2	chr9:26890200-26893400	Active TSS	Psoas Muscle	Psoas
3	chr9:26890200-26893600	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr9:26890400-26894400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr9:26890600-26893600	Active TSS	Fetal Intestine Small	intestine
6	chr9:26890600-26893600	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr9:26890800-26893600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:26890800-26893600	Active TSS	HSMM	muscle
9	chr9:26891000-26893400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr9:26891000-26893400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:26891000-26893400	Active TSS	Right Atrium	heart
12	chr9:26891000-26893600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:26891200-26893400	Active TSS	H1 Cell Line	embryonic stem cell
14	chr9:26891200-26893400	Active TSS	Fetal Heart	heart
15	chr9:26891200-26893600	Active TSS	Brain Anterior Caudate	brain
16	chr9:26891200-26893600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr9:26891400-26893400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:26891400-26893400	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr9:26891400-26893600	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr9:26891400-26893600	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr9:26891400-26893600	Bivalent/Poised TSS	HepG2	liver
22	chr9:26891600-26893400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr9:26891600-26893400	Active TSS	Fetal Brain Male	brain
24	chr9:26891600-26893400	Active TSS	Fetal Muscle Trunk	muscle
25	chr9:26891600-26893400	Active TSS	Sigmoid Colon	Sigmoid Colon
26	chr9:26891600-26893600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr9:26891800-26893400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr9:26891800-26893400	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr9:26891800-26893600	Active TSS	Brain Germinal Matrix	brain
30	chr9:26891800-26893600	Active TSS	Rectal Smooth Muscle	rectum
31	chr9:26891800-26893600	Active TSS	Stomach Smooth Muscle	stomach
32	chr9:26892000-26893600	Active TSS	Monocytes-CD14+_RO01746	blood
33	chr9:26892600-26893600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr9:26892800-26893400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr9:26892800-26893400	Flanking Active TSS	NH-A	brain
36	chr9:26892800-26916200	Weak transcription	Small Intestine	intestine
37	chr9:26893000-26893400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr9:26893000-26893400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chr9:26893000-26893400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr9:26893000-26893400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr9:26893000-26893400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr9:26893000-26893400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:26893000-26893400	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr9:26893000-26893400	Flanking Active TSS	Brain Hippocampus Middle	brain
45	chr9:26893000-26893400	Flanking Active TSS	Fetal Brain Female	brain
46	chr9:26893000-26893400	Enhancers	Gastric	stomach
47	chr9:26893000-26893400	Flanking Active TSS	Stomach Mucosa	stomach
48	chr9:26893000-26893400	Flanking Active TSS	HUVEC	blood vessel
49	chr9:26893000-26893400	Flanking Active TSS	NHDF-Ad	bronchial
50	chr9:26893000-26893600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links