Variant report

Variant	rs11053857
Chromosome Location	chr12:10707247-10707248
allele	A/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	RUNX3	chr12:10706530-10708273	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:10706642-10708188	GM12878	blood:	n/a	n/a
3	RUNX3	chr12:10706685-10707815	GM12878	blood:	n/a	n/a
4	MTA3	chr12:10706553-10708185	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:10706703-10708188	GM12878	blood:	n/a	n/a
6	CEBPB	chr12:10706586-10708245	GM12878	blood:	n/a	n/a
7	NFIC	chr12:10706546-10708335	GM12878	blood:	n/a	n/a
8	STAT5A	chr12:10706831-10708274	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:10707068-10707425	GM12891	blood:	n/a	n/a
10	POLR2A	chr12:10706657-10708164	GM12891	blood:	n/a	n/a
11	POLR2A	chr12:10706610-10708169	GM12891	blood:	n/a	n/a
12	BCLAF1	chr12:10706665-10707710	GM12878	blood:	n/a	n/a
13	MTA3	chr12:10706624-10708177	GM12878	blood:	n/a	n/a
14	STAT5A	chr12:10706704-10707902	GM12878	blood:	n/a	n/a
15	FOXM1	chr12:10706671-10708228	GM12878	blood:	n/a	n/a
16	NFATC1	chr12:10706609-10708281	GM12878	blood:	n/a	n/a
17	PML	chr12:10706604-10708141	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
SLC25A39P2	TF binding region

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10734838	0.82[ASN][1000 genomes]
rs10743910	0.82[ASN][1000 genomes]
rs10772298	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10772312	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10772315	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10772316	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10772317	0.83[ASN][1000 genomes]
rs10772319	0.82[ASN][1000 genomes]
rs10772321	0.82[ASN][1000 genomes]
rs10772323	0.82[ASN][1000 genomes]
rs10772324	0.83[ASN][1000 genomes]
rs10772325	0.81[ASN][1000 genomes]
rs10772326	0.82[ASN][1000 genomes]
rs10772327	0.82[ASN][1000 genomes]
rs10772329	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10845161	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845163	0.81[ASN][1000 genomes]
rs10845164	0.81[ASN][1000 genomes]
rs10845165	0.84[ASN][1000 genomes]
rs10845166	0.83[ASN][1000 genomes]
rs10845172	0.82[ASN][1000 genomes]
rs10845174	0.81[ASN][1000 genomes]
rs10845175	0.84[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11053859	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11053865	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11053869	0.82[ASN][1000 genomes]
rs11053870	0.82[ASN][1000 genomes]
rs11053871	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11611202	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12423957	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1915322	0.81[ASN][1000 genomes]
rs1915323	0.82[ASN][1000 genomes]
rs2002156	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2002157	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2125092	0.83[ASN][1000 genomes]
rs2125094	0.81[ASN][1000 genomes]
rs2125095	0.83[ASN][1000 genomes]
rs2168750	0.82[ASN][1000 genomes]
rs2417746	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs2417747	0.82[ASN][1000 genomes]
rs2417748	0.83[ASN][1000 genomes]
rs2607888	0.80[JPT][hapmap]
rs2607898	0.81[JPT][hapmap]
rs28403396	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28701155	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3816567	0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3867478	0.83[ASN][1000 genomes]
rs3983544	0.82[ASN][1000 genomes]
rs3983545	0.82[ASN][1000 genomes]
rs3983546	0.82[ASN][1000 genomes]
rs3983547	0.81[ASN][1000 genomes]
rs4237928	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4476009	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4763528	0.83[ASN][1000 genomes]
rs4763531	0.83[ASN][1000 genomes]
rs4763532	0.83[ASN][1000 genomes]
rs4763547	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4763548	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4763550	0.81[ASN][1000 genomes]
rs4763551	0.81[ASN][1000 genomes]
rs4763553	0.81[ASN][1000 genomes]
rs4763555	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4763559	0.82[ASN][1000 genomes]
rs55837119	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58917785	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60367665	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61913124	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6488306	0.90[JPT][hapmap]
rs6488307	0.82[ASN][1000 genomes]
rs7134658	0.82[ASN][1000 genomes]
rs7134908	0.82[ASN][1000 genomes]
rs7136964	0.81[ASN][1000 genomes]
rs7137465	0.81[ASN][1000 genomes]
rs7306285	0.82[ASN][1000 genomes]
rs7306724	0.84[ASN][1000 genomes]
rs7311860	0.81[ASN][1000 genomes]
rs7965052	0.81[ASN][1000 genomes]
rs7971934	0.81[ASN][1000 genomes]
rs7978850	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7980411	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898766	chr12:10537269-10722585	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv557459	chr12:10560591-10729821	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv898772	chr12:10622047-10722585	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv557479	chr12:10644663-10729821	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv898773	chr12:10660850-10722585	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv898774	chr12:10666025-10722585	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv898775	chr12:10668694-10735786	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv1039120	chr12:10675930-10755446	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv832329	chr12:10677094-10845946	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10706600-10707400	Enhancers	Dnd41	blood
2	chr12:10706800-10708000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
3	chr12:10706800-10708200	Flanking Active TSS	Primary T cells from cord blood	blood
4	chr12:10706800-10708200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:10706800-10708200	Flanking Active TSS	Fetal Thymus	thymus
6	chr12:10706800-10708200	ZNF genes & repeats	GM12878-XiMat	blood
7	chr12:10707000-10707400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
8	chr12:10707000-10707600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:10707000-10707800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:10707000-10707800	Enhancers	Primary hematopoietic stem cells	blood
11	chr12:10707000-10707800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:10707000-10708000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:10707000-10708000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr12:10707000-10708200	Active TSS	Thymus	Thymus
15	chr12:10707200-10707400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:10707200-10707600	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr12:10707200-10707600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:10707200-10707800	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr12:10707200-10708000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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