Variant report

Variant	rs12273949
Chromosome Location	chr11:63719525-63719526
allele	G/T
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	MAZ	chr11:63719167-63719754	GM12878	blood:	n/a	n/a
2	ATF2	chr11:63719292-63719704	GM12878	blood:	n/a	n/a
3	EBF1	chr11:63719114-63719688	GM12878	blood:	n/a	chr11:63719271-63719284 chr11:63719271-63719282 chr11:63719273-63719282
4	ATF2	chr11:63719266-63720002	GM12878	blood:	n/a	n/a
5	SP1	chr11:63719274-63719699	GM12878	blood:	n/a	n/a
6	POLR2A	chr11:63719365-63720216	GM12878	blood:	n/a	n/a
7	CHD2	chr11:63719317-63719767	GM12878	blood:	n/a	n/a
8	POU2F2	chr11:63719289-63720033	GM12878	blood:	n/a	n/a
9	POU2F2	chr11:63719381-63719989	GM12878	blood:	n/a	n/a
10	POLR2A	chr11:63719370-63720081	GM12878	blood:	n/a	n/a
11	EP300	chr11:63719344-63719692	GM12878	blood:	n/a	n/a
12	POLR2A	chr11:63719378-63719882	GM12878	blood:	n/a	n/a
13	POLR2A	chr11:63719285-63720262	GM12892	blood:	n/a	n/a
14	ELK1	chr11:63719432-63720047	GM12878	blood:	n/a	n/a
15	PML	chr11:63719442-63719679	GM12878	blood:	n/a	n/a
16	WRNIP1	chr11:63719201-63719845	GM12878	blood:	n/a	n/a
17	NFYB	chr11:63719499-63719797	GM12878	blood:	n/a	n/a
18	CHD1	chr11:63719319-63719944	GM12878	blood:	n/a	n/a
19	NFATC1	chr11:63719257-63719804	GM12878	blood:	n/a	n/a
20	RUNX3	chr11:63719093-63720159	GM12878	blood:	n/a	n/a
21	TAF1	chr11:63719381-63719619	GM12878	blood:	n/a	n/a
22	TBP	chr11:63719371-63719816	GM12878	blood:	n/a	n/a
23	NFIC	chr11:63719217-63719761	GM12878	blood:	n/a	n/a
24	ELF1	chr11:63719378-63720338	GM12878	blood:	n/a	n/a
25	EP300	chr11:63719389-63720060	GM12878	blood:	n/a	n/a
26	MAX	chr11:63719327-63719784	NB4	blood:	n/a	n/a
27	EBF1	chr11:63719106-63719604	GM12878	blood:	n/a	chr11:63719271-63719284 chr11:63719271-63719282 chr11:63719273-63719282
28	MTA3	chr11:63719226-63720169	GM12878	blood:	n/a	n/a
29	USF2	chr11:63719451-63719607	GM12878	blood:	n/a	n/a
30	PML	chr11:63719214-63719963	GM12878	blood:	n/a	n/a
31	RCOR1	chr11:63719393-63719681	GM12878	blood:	n/a	n/a
32	SPI1	chr11:63719414-63719805	GM12891	blood:	n/a	n/a
33	POLR2A	chr11:63719330-63719840	GM12892	blood:	n/a	n/a
34	POLR2A	chr11:63719270-63719804	GM12878	blood:	n/a	n/a
35	EBF1	chr11:63719082-63719820	GM12878	blood:	n/a	chr11:63719271-63719284 chr11:63719271-63719282 chr11:63719273-63719282
36	BHLHE40	chr11:63719388-63719687	GM12878	blood:	n/a	n/a
37	IKZF1	chr11:63719301-63720103	GM12878	blood:	n/a	n/a
38	ELF1	chr11:63719307-63720168	GM12878	blood:	n/a	n/a
39	STAT5A	chr11:63719286-63720185	GM12878	blood:	n/a	chr11:63719641-63719649 chr11:63719623-63719631 chr11:63719473-63719481
40	YY1	chr11:63719350-63719658	GM12878	blood:	n/a	n/a
41	TAF1	chr11:63719352-63719766	GM12878	blood:	n/a	n/a
42	SPI1	chr11:63719276-63719917	HL-60	blood:	n/a	n/a
43	MXI1	chr11:63719385-63719845	GM12878	blood:	n/a	n/a
44	POLR2A	chr11:63719321-63719982	GM12878	blood:	n/a	n/a
45	CEBPB	chr11:63719201-63719807	GM12878	blood:	n/a	n/a
46	MTA3	chr11:63719064-63720483	GM12878	blood:	n/a	n/a
47	IRF4	chr11:63719402-63720043	GM12878	blood:	n/a	n/a
48	SP1	chr11:63719291-63719712	GM12878	blood:	n/a	n/a
49	MYC	chr11:63719225-63719798	NB4	blood:	n/a	n/a
50	POLR2A	chr11:63719354-63719714	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:63705424..63708366-chr11:63719461..63721078,2	MCF-7	breast:

Variant related genes	Relation type
NAA40	TF binding region
ENSG00000110583	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11231647	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11231654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12272430	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12274488	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12274687	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12276514	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12284007	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12284291	0.86[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12285082	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12294590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34005543	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7103036	0.82[ASW][hapmap];0.93[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7936540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051171	chr11:62987064-63835715	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv468590	chr11:63639881-63783352	Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv555181	chr11:63639881-63783352	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv897629	chr11:63664882-63866959	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv897630	chr11:63664882-63924446	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv897631	chr11:63664882-64129722	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	254 gene(s)	inside rSNPs	diseases
7	nsv897639	chr11:63691049-63844683	Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	esv1849906	chr11:63719273-63880383	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12273949	JUP	trans	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63707200-63724200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:63707400-63719600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:63707400-63721400	Weak transcription	Small Intestine	intestine
4	chr11:63707600-63720200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:63707800-63719600	Weak transcription	Lung	lung
6	chr11:63708200-63723400	Weak transcription	NH-A	brain
7	chr11:63709600-63719600	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr11:63713200-63719800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr11:63713200-63719800	Weak transcription	Aorta	Aorta
10	chr11:63713200-63725400	Weak transcription	Psoas Muscle	Psoas
11	chr11:63713200-63725800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr11:63713400-63719600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr11:63713400-63719600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr11:63713400-63719800	Weak transcription	Brain Substantia Nigra	brain
15	chr11:63713400-63721200	Weak transcription	Stomach Mucosa	stomach
16	chr11:63713400-63721600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr11:63713400-63721600	Weak transcription	Ovary	ovary
18	chr11:63713400-63724200	Strong transcription	K562	blood
19	chr11:63713400-63725200	Strong transcription	Fetal Intestine Small	intestine
20	chr11:63713400-63725400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr11:63713400-63725800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:63713400-63726200	Strong transcription	Fetal Stomach	stomach
23	chr11:63713400-63726800	Weak transcription	Fetal Brain Male	brain
24	chr11:63713400-63733800	Weak transcription	Right Atrium	heart
25	chr11:63713600-63719600	Weak transcription	Colonic Mucosa	Colon
26	chr11:63713600-63719600	Strong transcription	Duodenum Mucosa	Duodenum
27	chr11:63713600-63719800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr11:63713600-63719800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr11:63713600-63719800	Weak transcription	HSMM	muscle
30	chr11:63713600-63723000	Weak transcription	Fetal Heart	heart
31	chr11:63713600-63724200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr11:63713600-63724200	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr11:63713600-63724400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr11:63713600-63725200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr11:63713600-63726000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr11:63713800-63724400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr11:63713800-63726000	Strong transcription	Fetal Muscle Leg	muscle
38	chr11:63714000-63726200	Strong transcription	Fetal Muscle Trunk	muscle
39	chr11:63714200-63719600	Weak transcription	Right Ventricle	heart
40	chr11:63714400-63719800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr11:63714400-63720000	Weak transcription	NHDF-Ad	bronchial
42	chr11:63714600-63719600	Weak transcription	Brain Angular Gyrus	brain
43	chr11:63714600-63719600	Weak transcription	Brain Anterior Caudate	brain
44	chr11:63714600-63719600	Weak transcription	Gastric	stomach
45	chr11:63714600-63719600	Weak transcription	Pancreas	Pancrea
46	chr11:63714600-63719800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr11:63714600-63719800	Weak transcription	Adipose Nuclei	Adipose
48	chr11:63714600-63719800	Weak transcription	Liver	Liver
49	chr11:63714600-63719800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr11:63714600-63719800	Weak transcription	Left Ventricle	heart

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