Variant report

Variant	rs854890
Chromosome Location	chr12:47474826-47474827
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	POLR2A	chr12:47474579-47474834	A549	lung:	n/a	n/a
2	HA-E2F1	chr12:47473081-47475013	MCF-7	breast:	n/a	chr12:47473414-47473424 chr12:47473420-47473430 chr12:47473770-47473779 chr12:47473819-47473829 chr12:47473789-47473799
3	EP300	chr12:47473651-47475489	ECC-1	luminal epithelium:	n/a	chr12:47473821-47473830 chr12:47474101-47474110 chr12:47473816-47473825 chr12:47473738-47473754 chr12:47473788-47473797
4	POLR2A	chr12:47473900-47475357	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr12:47473147-47474855	MCF-7	breast:	n/a	n/a
6	MYC	chr12:47472611-47475219	K562	blood:	n/a	chr12:47473840-47473850
7	BRCA1	chr12:47473739-47475291	Hela-S3	cervix:	n/a	n/a
8	E2F4	chr12:47474234-47475240	MCF10A-Er-Src	breast:	n/a	n/a
9	ZNF263	chr12:47472679-47474962	HEK293-T-REx	kidney:	n/a	chr12:47474274-47474295 chr12:47474273-47474282 chr12:47473855-47473864 chr12:47474441-47474450
10	TEAD4	chr12:47474065-47475371	A549	lung:	n/a	n/a
11	PRDM1	chr12:47474051-47475621	Hela-S3	cervix:	n/a	chr12:47475127-47475136 chr12:47475122-47475137
12	SIN3AK20	chr12:47473556-47475236	A549	lung:	n/a	n/a
13	EP300	chr12:47473587-47475637	A549	lung:	n/a	chr12:47473821-47473830 chr12:47474101-47474110 chr12:47473816-47473825 chr12:47473738-47473754 chr12:47473788-47473797
14	POLR2A	chr12:47473830-47475129	PFSK-1	brain:	n/a	n/a
15	SIN3AK20	chr12:47473758-47475029	MCF-7	breast:	n/a	n/a
16	BCL3	chr12:47473705-47477622	A549	lung:	n/a	chr12:47473792-47473801 chr12:47473789-47473798 chr12:47475153-47475162 chr12:47473839-47473852
17	POLR2A	chr12:47473161-47474891	PANC-1	pancreas:	n/a	n/a
18	ATF3	chr12:47473477-47474870	A549	lung:	n/a	chr12:47473656-47473665 chr12:47474252-47474263 chr12:47474104-47474124 chr12:47474250-47474263
19	TBP	chr12:47473924-47475381	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr12:47474556-47474878	A549	lung:	n/a	n/a
21	GABPA	chr12:47473978-47474947	A549	lung:	n/a	n/a
22	MAZ	chr12:47473162-47475387	Hela-S3	cervix:	n/a	chr12:47473840-47473850
23	TAF1	chr12:47473058-47474879	MCF-7	breast:	n/a	n/a
24	ZNF143	chr12:47474063-47474865	Hela-S3	cervix:	n/a	n/a
25	FOSL2	chr12:47473771-47475676	A549	lung:	n/a	chr12:47474904-47474912 chr12:47475154-47475161 chr12:47474902-47474914
26	POLR2A	chr12:47473091-47474907	A549	lung:	n/a	n/a
27	E2F6	chr12:47473576-47475287	A549	lung:	n/a	chr12:47473770-47473779 chr12:47473819-47473829 chr12:47473789-47473799
28	SMARCB1	chr12:47472539-47475076	Hela-S3	cervix:	n/a	chr12:47474903-47474912
29	POLR2A	chr12:47474544-47474856	A549	lung:	n/a	n/a
30	PBX3	chr12:47473554-47474946	A549	lung:	n/a	n/a
31	CEBPB	chr12:47473991-47475416	A549	lung:	n/a	n/a
32	RAD21	chr12:47473864-47475321	A549	lung:	n/a	n/a
33	MAZ	chr12:47473113-47475229	K562	blood:	n/a	chr12:47473840-47473850
34	MAX	chr12:47472652-47475311	Hela-S3	cervix:	n/a	chr12:47473840-47473850
35	BHLHE40	chr12:47473944-47475249	K562	blood:	n/a	n/a
36	POLR2A	chr12:47473183-47474848	MCF-7	breast:	n/a	n/a
37	TCF12	chr12:47473728-47475328	ECC-1	luminal epithelium:	n/a	n/a
38	MYC	chr12:47474457-47475240	MCF10A-Er-Src	breast:	n/a	n/a
39	NR3C1	chr12:47474525-47474915	A549	lung:	n/a	chr12:47474777-47474792 chr12:47474904-47474913
40	SIN3AK20	chr12:47473810-47475406	A549	lung:	n/a	n/a
41	IRF1	chr12:47474467-47475213	K562	blood:	n/a	n/a
42	EP300	chr12:47473590-47475574	A549	lung:	n/a	chr12:47473821-47473830 chr12:47474101-47474110 chr12:47473816-47473825 chr12:47473738-47473754 chr12:47473788-47473797
43	ETS1	chr12:47473782-47475359	A549	lung:	n/a	chr12:47474473-47474486 chr12:47473789-47473800 chr12:47474332-47474345 chr12:47475085-47475096 chr12:47473786-47473797 chr12:47474476-47474485 chr12:47474334-47474341 chr12:47473917-47473928
44	ELK1	chr12:47474061-47475185	Hela-S3	cervix:	n/a	n/a
45	SIN3AK20	chr12:47473631-47475447	MCF-7	breast:	n/a	n/a
46	SP1	chr12:47470742-47475642	A549	lung:	n/a	chr12:47473708-47473722 chr12:47473736-47473749 chr12:47475085-47475094 chr12:47475083-47475095 chr12:47473915-47473929 chr12:47473912-47473924 chr12:47473913-47473922 chr12:47473787-47473799 chr12:47472827-47472841 chr12:47473912-47473924
47	REST	chr12:47473737-47475311	A549	lung:	n/a	chr12:47473907-47473920
48	MAX	chr12:47474492-47474885	K562	blood:	n/a	n/a
49	POLR2A	chr12:47474537-47474856	A549	lung:	n/a	n/a
50	YY1	chr12:47473569-47474929	A549	lung:	n/a	chr12:47473920-47473931 chr12:47473816-47473830 chr12:47473788-47473797 chr12:47473791-47473805 chr12:47473783-47473797 chr12:47473839-47473848 chr12:47473791-47473800 chr12:47473785-47473799

No.	Distal block	Cell Line	Cell type
1	chr12:47472804..47476649-chr12:47581153..47583704,4	MCF-7	breast:
2	chr12:47474204..47478207-chr12:47669855..47672780,4	MCF-7	breast:
3	chr12:47473378..47475019-chr12:47616001..47619116,3	MCF-7	breast:
4	chr12:47474476..47477081-chr12:47578294..47580063,2	MCF-7	breast:
5	chr12:47474456..47476643-chr12:47638235..47640593,2	MCF-7	breast:
6	chr12:47473622..47475648-chr12:47613193..47617300,3	MCF-7	breast:

Variant related genes	Relation type
AMIGO2	TF binding region
ENSG00000263838	Chromatin interaction
ENSG00000179715	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1101753	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4768771	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs854888	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs854889	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][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	nsv469368	chr12:47374908-47675680	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv558784	chr12:47374908-47675680	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47470000-47475000	Active TSS	Colon Smooth Muscle	Colon
2	chr12:47470800-47475000	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr12:47471600-47475200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:47472000-47475200	Active TSS	Stomach Smooth Muscle	stomach
5	chr12:47472200-47475000	Active TSS	Muscle Satellite Cultured Cells	--
6	chr12:47472200-47475000	Active TSS	Aorta	Aorta
7	chr12:47472200-47475000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:47472400-47475000	Active TSS	Ovary	ovary
9	chr12:47472600-47475000	Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr12:47472600-47475200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:47472800-47475000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
12	chr12:47472800-47475000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:47472800-47475000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
14	chr12:47472800-47475000	Active TSS	Brain Cingulate Gyrus	brain
15	chr12:47472800-47475000	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr12:47472800-47475000	Active TSS	Right Atrium	heart
17	chr12:47472800-47475200	Active TSS	HSMM	muscle
18	chr12:47472800-47475800	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr12:47473000-47475000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:47473000-47475000	Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr12:47473000-47475000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:47473000-47475000	Active TSS	Brain Hippocampus Middle	brain
23	chr12:47473000-47475200	Active TSS	Fetal Kidney	kidney
24	chr12:47473200-47475000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr12:47473200-47475000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
26	chr12:47473200-47475200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:47473200-47475200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
28	chr12:47473200-47475200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr12:47473200-47475200	Active TSS	Rectal Smooth Muscle	rectum
30	chr12:47473200-47475400	Active TSS	A549	lung
31	chr12:47473400-47475000	Active TSS	Brain Angular Gyrus	brain
32	chr12:47473400-47475000	Active TSS	Rectal Mucosa Donor 31	rectum
33	chr12:47473800-47475000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
34	chr12:47473800-47475000	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr12:47473800-47475000	Active TSS	Colonic Mucosa	Colon
36	chr12:47473800-47475200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:47473800-47475200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:47473800-47475200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr12:47473800-47475200	Flanking Active TSS	HUVEC	blood vessel
40	chr12:47473800-47475400	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr12:47474000-47475000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr12:47474000-47475000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr12:47474000-47475000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:47474000-47475000	Flanking Active TSS	K562	blood
45	chr12:47474000-47475200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
46	chr12:47474000-47475400	Flanking Active TSS	Osteobl	bone
47	chr12:47474400-47475000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:47474400-47475000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:47474400-47475000	Active TSS	Duodenum Mucosa	Duodenum
50	chr12:47474400-47475000	Active TSS	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links