Variant report

Variant	rs12471472
Chromosome Location	chr2:96205455-96205456
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	MTA3	chr2:96205338-96205945	GM12878	blood:	n/a	n/a
2	MTA3	chr2:96205359-96206046	GM12878	blood:	n/a	n/a
3	IRF4	chr2:96205429-96205964	GM12878	blood:	n/a	n/a
4	EP300	chr2:96205211-96205902	GM12878	blood:	n/a	n/a
5	MEF2A	chr2:96205384-96205966	GM12878	blood:	n/a	n/a
6	NFIC	chr2:96205283-96205992	GM12878	blood:	n/a	n/a
7	PML	chr2:96205426-96205984	GM12878	blood:	n/a	n/a
8	RCOR1	chr2:96205254-96205957	GM12878	blood:	n/a	n/a
9	MAZ	chr2:96205387-96205876	GM12878	blood:	n/a	n/a
10	NFIC	chr2:96204950-96206156	GM12878	blood:	n/a	n/a
11	MEF2A	chr2:96205339-96205955	GM12878	blood:	n/a	n/a
12	BCLAF1	chr2:96205437-96206099	GM12878	blood:	n/a	n/a
13	ATF2	chr2:96205376-96206066	GM12878	blood:	n/a	n/a
14	BATF	chr2:96205451-96205899	GM12878	blood:	n/a	n/a
15	SPI1	chr2:96205259-96206108	GM12878	blood:	n/a	n/a
16	IRF4	chr2:96205436-96206053	GM12878	blood:	n/a	n/a
17	RUNX3	chr2:96205419-96206022	GM12878	blood:	n/a	n/a
18	PAX5	chr2:96205445-96206076	GM12878	blood:	n/a	n/a
19	FOXM1	chr2:96205384-96206091	GM12878	blood:	n/a	n/a
20	BCL11A	chr2:96205442-96205930	GM12878	blood:	n/a	n/a
21	MEF2C	chr2:96205386-96205910	GM12878	blood:	n/a	n/a
22	JUND	chr2:96205450-96206174	GM12878	blood:	n/a	n/a
23	SP1	chr2:96205454-96206025	GM12878	blood:	n/a	n/a
24	FOXM1	chr2:96205370-96206014	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000236431	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10874471	0.86[JPT][hapmap];0.82[YRI][hapmap]
rs11164125	0.95[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes]
rs11677429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12468117	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12468777	0.86[JPT][hapmap];0.82[YRI][hapmap]
rs1345917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1364394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1834135	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2216793	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2320170	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2320431	0.86[JPT][hapmap]
rs3755518	0.86[JPT][hapmap]
rs3772031	0.82[YRI][hapmap]
rs3772032	0.82[YRI][hapmap]
rs3772033	0.82[YRI][hapmap]
rs3866290	0.81[AMR][1000 genomes]
rs4854251	0.86[JPT][hapmap]
rs4854253	0.95[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs4907303	0.87[AFR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67628541	0.85[AMR][1000 genomes]
rs72821422	0.88[AMR][1000 genomes]
rs72821437	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs869185	0.86[JPT][hapmap]
rs9678800	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv998014	chr2:95913278-96296630	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv3416818	chr2:96072529-96680708	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv834300	chr2:96087967-96337557	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv874660	chr2:96091132-96669134	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
6	nsv516044	chr2:96150959-96683378	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
7	nsv1006283	chr2:96159804-96206863	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001305	chr2:96161688-96259200	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1008062	chr2:96166970-96259200	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv998984	chr2:96166970-96290275	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv998587	chr2:96170558-96378228	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv979062	chr2:96199535-96212061	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12471472	AC008268.1	cis	lung	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96194400-96207200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:96197800-96205800	Weak transcription	NHDF-Ad	bronchial
3	chr2:96198200-96207400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:96203800-96205600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:96204800-96205600	Enhancers	Osteobl	bone
6	chr2:96204800-96205800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:96204800-96205800	Enhancers	Muscle Satellite Cultured Cells	--
8	chr2:96205400-96205800	Active TSS	GM12878-XiMat	blood

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