Variant report

Variant	rs12692450
Chromosome Location	chr2:12147176-12147177
allele	C/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	CHD2	chr2:12146958-12147585	H1-hESC	embryonic stem cell:	n/a	n/a
2	FOS	chr2:12147083-12147572	HUVEC	blood vessel:	n/a	n/a
3	CEBPB	chr2:12147057-12147355	A549	lung:	n/a	n/a
4	MAX	chr2:12147077-12147350	H1-hESC	embryonic stem cell:	n/a	n/a
5	CEBPB	chr2:12147149-12147268	Hela-S3	cervix:	n/a	n/a
6	MAX	chr2:12147054-12147937	H1-hESC	embryonic stem cell:	n/a	n/a
7	CEBPB	chr2:12147115-12147347	ECC-1	luminal epithelium:	n/a	n/a
8	ATF2	chr2:12146969-12147467	H1-hESC	embryonic stem cell:	n/a	n/a
9	JUN	chr2:12147018-12147358	HUVEC	blood vessel:	n/a	chr2:12147192-12147205
10	CEBPB	chr2:12147042-12147348	K562	blood:	n/a	n/a
11	TEAD4	chr2:12146986-12147429	ECC-1	luminal epithelium:	n/a	chr2:12147182-12147191
12	FOS	chr2:12147146-12147202	MCF10A-Er-Src	breast:	n/a	n/a
13	TEAD4	chr2:12146911-12147459	H1-hESC	embryonic stem cell:	n/a	chr2:12147182-12147191
14	CEBPB	chr2:12147015-12147377	IMR90	lung:	n/a	n/a
15	CEBPB	chr2:12147022-12147374	HepG2	liver:	n/a	n/a
16	FOS	chr2:12147174-12147337	MCF10A-Er-Src	breast:	n/a	n/a
17	ATF2	chr2:12146952-12147399	H1-hESC	embryonic stem cell:	n/a	n/a
18	JUN	chr2:12147017-12147374	HepG2	liver:	n/a	chr2:12147192-12147205
19	YY1	chr2:12147034-12147412	H1-hESC	embryonic stem cell:	n/a	n/a
20	CEBPB	chr2:12147016-12147393	H1-hESC	embryonic stem cell:	n/a	n/a
21	JUN	chr2:12146973-12147447	H1-hESC	embryonic stem cell:	n/a	chr2:12147192-12147205
22	TEAD4	chr2:12147008-12147412	H1-hESC	embryonic stem cell:	n/a	chr2:12147182-12147191
23	JUND	chr2:12146990-12147337	H1-hESC	embryonic stem cell:	n/a	n/a
24	JUND	chr2:12146585-12147454	H1-hESC	embryonic stem cell:	n/a	n/a
25	KAP1	chr2:12146917-12147478	HEK293	kidney:	n/a	n/a
26	TEAD4	chr2:12146990-12147427	ECC-1	luminal epithelium:	n/a	chr2:12147182-12147191
27	JUND	chr2:12147093-12147301	H1-hESC	embryonic stem cell:	n/a	n/a
28	JUND	chr2:12147040-12147370	K562	blood:	n/a	n/a
29	JUND	chr2:12147009-12147382	HepG2	liver:	n/a	n/a
30	ATF3	chr2:12146983-12147363	H1-hESC	embryonic stem cell:	n/a	chr2:12147196-12147207 chr2:12147194-12147207 chr2:12147196-12147204 chr2:12147193-12147208

Variant related genes	Relation type
ENSG00000224184	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10199352	0.98[ASN][1000 genomes]
rs11897150	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12692451	0.98[ASN][1000 genomes]
rs1371613	0.96[ASN][1000 genomes]
rs6727216	0.97[ASN][1000 genomes]
rs9646725	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs966367	0.97[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	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	esv3433991	chr2:12146727-12147182	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12692450	GREB1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:12137200-12148800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:12141400-12147200	Weak transcription	K562	blood
3	chr2:12144600-12147200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr2:12145000-12147200	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr2:12145000-12147200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr2:12145000-12147400	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr2:12145000-12147400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:12145000-12147600	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr2:12145000-12149800	Enhancers	Primary B cells from peripheral blood	blood
10	chr2:12145200-12147200	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr2:12145200-12147600	Enhancers	HUVEC	blood vessel
12	chr2:12145400-12147800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr2:12145600-12147200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr2:12145600-12147400	Enhancers	Fetal Lung	lung
15	chr2:12145600-12147400	Enhancers	Fetal Muscle Leg	muscle
16	chr2:12145600-12147600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:12145600-12147600	Enhancers	NH-A	brain
18	chr2:12145600-12147800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:12145600-12147800	Enhancers	HSMM	muscle
20	chr2:12145800-12147400	Enhancers	Fetal Heart	heart
21	chr2:12145800-12147400	Enhancers	HMEC	breast
22	chr2:12145800-12147400	Enhancers	Osteobl	bone
23	chr2:12145800-12148000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:12145800-12148000	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr2:12146000-12147400	Enhancers	Fetal Stomach	stomach
26	chr2:12146000-12147600	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr2:12146000-12148000	Enhancers	Liver	Liver
28	chr2:12146200-12147200	Enhancers	NHEK	skin
29	chr2:12146200-12147400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:12146200-12147600	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr2:12146200-12147600	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr2:12146200-12147600	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr2:12146200-12147800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:12146400-12147200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr2:12146400-12147800	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr2:12146400-12148000	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr2:12146400-12148000	Weak transcription	NHLF	lung
38	chr2:12146400-12151000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:12146600-12147200	Enhancers	Fetal Kidney	kidney
40	chr2:12146600-12147400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:12146600-12147400	Weak transcription	Fetal Brain Female	brain
42	chr2:12146600-12147600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:12146600-12148000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:12146600-12148800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:12146600-12148800	Enhancers	GM12878-XiMat	blood
46	chr2:12146600-12148800	Weak transcription	HSMMtube	muscle
47	chr2:12146600-12153600	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr2:12146800-12147200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
49	chr2:12146800-12147400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:12146800-12147400	Enhancers	Muscle Satellite Cultured Cells	--

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