Variant report

Variant	rs11239300
Chromosome Location	chr10:45474154-45474155
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	SRF	chr10:45473877-45474735	HCT-116	colon:	n/a	chr10:45474367-45474377
2	POLR2A	chr10:45473685-45474581	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr10:45473991-45474489	MCF-7	breast:	n/a	n/a
4	SRF	chr10:45474078-45474508	HepG2	liver:	n/a	chr10:45474367-45474377
5	TAF1	chr10:45474135-45474334	GM12892	blood:	n/a	n/a
6	POLR2A	chr10:45474072-45474354	A549	lung:	n/a	n/a
7	SRF	chr10:45474082-45474645	ECC-1	luminal epithelium:	n/a	chr10:45474367-45474377
8	USF1	chr10:45474076-45474559	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr10:45470953-45474705	HepG2	liver:	n/a	n/a
10	TCF12	chr10:45474003-45474748	SK-N-SH	brain:	n/a	chr10:45474045-45474055
11	MAFK	chr10:45474141-45474449	HepG2	liver:	n/a	n/a
12	MBD4	chr10:45473974-45474697	HepG2	liver:	n/a	n/a
13	POLR2A	chr10:45473983-45474432	HEK293	kidney:	n/a	n/a
14	HEY1	chr10:45470947-45474495	HepG2	liver:	n/a	n/a
15	SRF	chr10:45473824-45474795	MCF-7	breast:	n/a	chr10:45474367-45474377
16	KAP1	chr10:45473875-45474719	U2OS	brain:	n/a	n/a
17	HCFC1	chr10:45474118-45474705	K562	blood:	n/a	n/a
18	STAT5A	chr10:45473889-45474499	GM12878	blood:	n/a	n/a
19	MXI1	chr10:45474119-45474393	K562	blood:	n/a	n/a
20	MYBL2	chr10:45470920-45474664	HepG2	liver:	n/a	n/a
21	EP300	chr10:45473669-45474609	K562	blood:	n/a	chr10:45474007-45474017
22	POU2F2	chr10:45473931-45474519	GM12878	blood:	n/a	n/a
23	POLR2A	chr10:45474033-45474579	K562	blood:	n/a	n/a
24	POLR2A	chr10:45471121-45474585	GM19193	blood:	n/a	n/a
25	MAFF	chr10:45474070-45474522	HepG2	liver:	n/a	n/a
26	POLR2A	chr10:45474011-45474446	GM12891	blood:	n/a	n/a
27	POLR2A	chr10:45474124-45474301	A549	lung:	n/a	n/a
28	MAFK	chr10:45474116-45474524	K562	blood:	n/a	n/a
29	NFIC	chr10:45473980-45474448	GM12878	blood:	n/a	n/a
30	USF1	chr10:45473979-45474503	HepG2	liver:	n/a	n/a
31	POLR2A	chr10:45473937-45474474	ProgFib	skin:	n/a	n/a
32	FOSL2	chr10:45473879-45474566	HepG2	liver:	n/a	n/a
33	EP300	chr10:45474138-45474476	SK-N-SH_RA	brain:	n/a	n/a
34	BRCA1	chr10:45474041-45474581	HepG2	liver:	n/a	n/a
35	MEF2C	chr10:45474011-45474574	GM12878	blood:	n/a	chr10:45474319-45474334 chr10:45474321-45474335 chr10:45474316-45474337 chr10:45474323-45474334 chr10:45474322-45474333
36	STAT1	chr10:45473680-45474517	GM12878	blood:	n/a	chr10:45474488-45474500
37	EP300	chr10:45474098-45474643	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr10:45473271-45474480	IMR90	lung:	n/a	n/a
39	PML	chr10:45474085-45474393	GM12878	blood:	n/a	n/a
40	STAT3	chr10:45473839-45474918	MCF10A-Er-Src	breast:	n/a	chr10:45474488-45474500 chr10:45474289-45474300
41	EP300	chr10:45474109-45474452	GM12878	blood:	n/a	n/a
42	MAZ	chr10:45473828-45474517	GM12878	blood:	n/a	chr10:45474367-45474377
43	HMGN3	chr10:45474051-45474619	K562	blood:	n/a	n/a
44	POLR2A	chr10:45470342-45475147	HepG2	liver:	n/a	n/a
45	JUN	chr10:45473859-45474967	K562	blood:	n/a	n/a
46	POLR2A	chr10:45473918-45474830	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr10:45473896-45474549	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr10:45466844-45474598	HepG2	liver:	n/a	n/a
49	TBL1XR1	chr10:45474078-45474352	K562	blood:	n/a	n/a
50	REST	chr10:45474131-45474382	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:45472874..45476114-chr10:45485945..45489321,3	MCF-7	breast:
2	chr10:45472768..45475523-chr10:45475664..45479867,4	MCF-7	breast:
3	chr10:45424948..45427085-chr10:45472059..45474210,2	K562	blood:
4	chr10:45472874..45475868-chr10:45493532..45497096,3	K562	blood:
5	chr10:45473658..45475931-chr10:46089040..46091906,2	K562	blood:
6	chr10:45469560..45475620-chr10:45475961..45481693,7	MCF-7	breast:
7	chr10:45472274..45474352-chr10:45475240..45477414,3	K562	blood:
8	chr10:45474000..45475702-chr10:45494679..45496847,2	MCF-7	breast:
9	chr10:45452399..45456775-chr10:45472666..45475790,4	MCF-7	breast:
10	chr10:45424948..45428447-chr10:45472059..45474990,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C10orf10-3	chr10:45474066-45474238	NONHSAT013051

Variant related genes	Relation type
RASSF4	TF binding region
ENSG00000224812	Chromatin interaction
ENSG00000165511	Chromatin interaction
ENSG00000107551	Chromatin interaction
ENSG00000165406	Chromatin interaction
ENSG00000187783	Chromatin interaction
ENSG00000165512	Chromatin interaction
ENSG00000273363	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11815349	1.00[EUR][1000 genomes]
rs11816338	1.00[EUR][1000 genomes]
rs12249378	1.00[EUR][1000 genomes]
rs12250724	1.00[EUR][1000 genomes]
rs12251910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17157321	0.95[AFR][1000 genomes]
rs56413731	1.00[EUR][1000 genomes]
rs57792208	1.00[EUR][1000 genomes]
rs58731194	0.95[AFR][1000 genomes]
rs7068974	0.81[AFR][1000 genomes]
rs7085359	1.00[EUR][1000 genomes]
rs7095998	1.00[EUR][1000 genomes]
rs73275092	1.00[EUR][1000 genomes]
rs73287594	1.00[EUR][1000 genomes]
rs74128124	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74131512	1.00[EUR][1000 genomes]
rs74131513	1.00[EUR][1000 genomes]
rs7898705	1.00[EUR][1000 genomes]
rs7899617	1.00[EUR][1000 genomes]
rs7900196	1.00[EUR][1000 genomes]
rs7903078	1.00[EUR][1000 genomes]
rs7903359	1.00[EUR][1000 genomes]
rs7924266	1.00[EUR][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	nsv831846	chr10:45322236-45556370	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv526734	chr10:45458485-45492054	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45470600-45474200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr10:45470800-45474400	Active TSS	Right Atrium	heart
3	chr10:45470800-45476400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr10:45470800-45477800	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr10:45470800-45479400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr10:45471200-45474600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr10:45471400-45474400	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle
8	chr10:45471400-45476600	Enhancers	H1 Cell Line	embryonic stem cell
9	chr10:45471600-45476800	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr10:45471800-45474200	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
11	chr10:45472200-45474400	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr10:45472600-45474200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr10:45472600-45474200	Active TSS	Gastric	stomach
14	chr10:45472600-45474200	Active TSS	Small Intestine	intestine
15	chr10:45472600-45474400	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr10:45472600-45474400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
17	chr10:45472600-45474800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr10:45472800-45474200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
19	chr10:45472800-45474400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr10:45472800-45474400	Active TSS	Liver	Liver
21	chr10:45472800-45474400	Genic enhancers	Monocytes-CD14+_RO01746	blood
22	chr10:45472800-45474600	Flanking Active TSS	Osteobl	bone
23	chr10:45473000-45474200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr10:45473000-45474200	Bivalent/Poised TSS	HepG2	liver
25	chr10:45473000-45474400	Active TSS	NHDF-Ad	bronchial
26	chr10:45473000-45474600	Flanking Active TSS	HSMM	muscle
27	chr10:45473000-45477800	Enhancers	Placenta Amnion	Placenta Amnion
28	chr10:45473200-45474200	Active TSS	Aorta	Aorta
29	chr10:45473200-45474200	Flanking Active TSS	Brain Substantia Nigra	brain
30	chr10:45473200-45474200	Flanking Active TSS	Fetal Heart	heart
31	chr10:45473200-45474200	Flanking Active TSS	HUVEC	blood vessel
32	chr10:45473200-45474400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr10:45473200-45474400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr10:45473200-45474400	Flanking Active TSS	Brain Angular Gyrus	brain
35	chr10:45473200-45474600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr10:45473200-45475000	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr10:45473400-45474200	Flanking Active TSS	Fetal Intestine Large	intestine
38	chr10:45473400-45474200	Flanking Active TSS	Fetal Intestine Small	intestine
39	chr10:45473400-45474200	Active TSS	Spleen	Spleen
40	chr10:45473400-45474400	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr10:45473400-45474400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr10:45473400-45474400	Genic enhancers	Primary monocytes fromperipheralblood	blood
43	chr10:45473400-45474400	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr10:45473400-45474600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
45	chr10:45473400-45474600	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr10:45473400-45474800	Flanking Active TSS	Brain Anterior Caudate	brain
47	chr10:45473400-45474800	Flanking Active TSS	Placenta	Placenta
48	chr10:45473400-45475200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr10:45473600-45474200	Flanking Active TSS	Fetal Kidney	kidney
50	chr10:45473600-45474200	Active TSS	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links