Variant report

Variant	rs11058789
Chromosome Location	chr12:122651418-122651419
allele	C/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	chr12:122650726-122651910	GM12878	blood:	n/a	n/a
2	STAT1	chr12:122651120-122651481	GM12878	blood:	n/a	chr12:122651438-122651450
3	TCF12	chr12:122651236-122651506	GM12878	blood:	n/a	n/a
4	STAT5A	chr12:122650861-122651719	GM12878	blood:	n/a	chr12:122651438-122651450
5	PML	chr12:122650825-122652091	GM12878	blood:	n/a	chr12:122651399-122651408
6	BATF	chr12:122650732-122651988	GM12878	blood:	n/a	chr12:122651398-122651409 chr12:122651399-122651409
7	NFATC1	chr12:122650828-122651656	GM12878	blood:	n/a	n/a
8	WRNIP1	chr12:122650999-122651673	GM12878	blood:	n/a	n/a
9	MXI1	chr12:122650967-122651453	GM12878	blood:	n/a	n/a
10	ATF2	chr12:122650795-122651922	GM12878	blood:	n/a	n/a
11	TBL1XR1	chr12:122650952-122651568	GM12878	blood:	n/a	n/a
12	BCLAF1	chr12:122650899-122651847	GM12878	blood:	n/a	chr12:122651818-122651827
13	MEF2C	chr12:122650710-122651573	GM12878	blood:	n/a	chr12:122651398-122651406
14	IKZF1	chr12:122650816-122651708	GM12878	blood:	n/a	n/a
15	EBF1	chr12:122650967-122651861	GM12878	blood:	n/a	n/a
16	JUND	chr12:122651303-122651484	K562	blood:	n/a	chr12:122651399-122651406 chr12:122651398-122651406 chr12:122651397-122651407 chr12:122651398-122651406 chr12:122651396-122651408
17	ZNF143	chr12:122651051-122651446	GM12878	blood:	n/a	n/a
18	BCL3	chr12:122651181-122651537	GM12878	blood:	n/a	n/a
19	STAT5A	chr12:122650833-122651650	GM12878	blood:	n/a	chr12:122651438-122651450
20	EP300	chr12:122650966-122651660	GM12878	blood:	n/a	chr12:122651397-122651406
21	POU2F2	chr12:122650947-122651531	GM12891	blood:	n/a	n/a
22	NFIC	chr12:122650550-122651918	GM12878	blood:	n/a	n/a
23	ELF1	chr12:122651113-122651887	GM12878	blood:	n/a	n/a
24	MAX	chr12:122651021-122651462	GM12878	blood:	n/a	chr12:122651397-122651406
25	RELA	chr12:122651015-122651637	GM19193	blood:	n/a	n/a
26	IRF4	chr12:122650746-122651725	GM12878	blood:	n/a	n/a
27	ATF2	chr12:122650854-122651884	GM12878	blood:	n/a	n/a
28	MTA3	chr12:122650761-122652090	GM12878	blood:	n/a	n/a
29	SMC3	chr12:122651128-122651489	GM12878	blood:	n/a	n/a
30	EBF1	chr12:122651274-122652005	GM12878	blood:	n/a	n/a
31	MTA3	chr12:122650825-122652190	GM12878	blood:	n/a	n/a
32	YY1	chr12:122650879-122651488	GM12878	blood:	n/a	n/a
33	MEF2A	chr12:122650824-122651615	GM12878	blood:	n/a	chr12:122651398-122651406
34	JUND	chr12:122650803-122651646	GM12878	blood:	n/a	chr12:122651399-122651406 chr12:122651398-122651406 chr12:122651397-122651407 chr12:122651398-122651406 chr12:122651396-122651408
35	BCL11A	chr12:122650793-122651656	GM12878	blood:	n/a	n/a
36	FOXM1	chr12:122650717-122652052	GM12878	blood:	n/a	n/a
37	BHLHE40	chr12:122650947-122651609	GM12878	blood:	n/a	n/a
38	SP1	chr12:122650819-122651542	GM12878	blood:	n/a	n/a
39	BCLAF1	chr12:122650777-122651634	GM12878	blood:	n/a	n/a
40	RUNX3	chr12:122650284-122652055	GM12878	blood:	n/a	n/a
41	NRF1	chr12:122651298-122651562	GM12878	blood:	n/a	n/a
42	PAX5	chr12:122650943-122651630	GM12878	blood:	n/a	n/a
43	FOXM1	chr12:122650814-122651888	GM12878	blood:	n/a	n/a
44	RCOR1	chr12:122651175-122651639	GM12878	blood:	n/a	n/a
45	NFIC	chr12:122650749-122651759	GM12878	blood:	n/a	n/a
46	EP300	chr12:122650976-122651603	GM12878	blood:	n/a	chr12:122651397-122651406
47	CEBPB	chr12:122650786-122651993	GM12878	blood:	n/a	n/a
48	TCF12	chr12:122651253-122651796	GM12878	blood:	n/a	n/a
49	BATF	chr12:122650852-122651587	GM12878	blood:	n/a	chr12:122651398-122651409 chr12:122651399-122651409
50	IRF4	chr12:122650788-122651680	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
LRRC43	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10847516	0.82[ASN][1000 genomes]
rs11058587	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11059472	0.86[ASN][1000 genomes]
rs11059505	0.88[CEU][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs11059675	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11608363	0.85[ASN][1000 genomes]
rs11611988	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11613060	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12816786	0.82[ASN][1000 genomes]
rs12828783	0.87[CEU][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs34402328	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4040811	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4319543	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4372487	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61954257	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6489217	0.86[ASN][1000 genomes]
rs6489244	0.82[MEX][hapmap]
rs7953139	0.86[ASN][1000 genomes]
rs7955910	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7968808	0.88[ASW][hapmap];0.96[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7972875	0.87[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs7972979	0.88[CEU][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv527450	chr12:122481290-122676531	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1038827	chr12:122627371-122687913	Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11058789	GPR81	cis	cerebellum	SCAN
rs11058789	PRKAB1	cis	cerebellum	SCAN
rs11058789	P2RX4	cis	parietal	SCAN
rs11058789	FAM101A	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122630600-122655600	Weak transcription	Right Ventricle	heart
2	chr12:122650600-122652400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
3	chr12:122651000-122651800	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr12:122651000-122652000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:122651000-122652000	Flanking Active TSS	GM12878-XiMat	blood
6	chr12:122651000-122652200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:122651200-122651600	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr12:122651200-122651600	Enhancers	Duodenum Mucosa	Duodenum
9	chr12:122651200-122651800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:122651200-122651800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:122651200-122652200	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr12:122651200-122652400	Enhancers	Fetal Intestine Large	intestine
13	chr12:122651400-122652200	Flanking Bivalent TSS/Enh	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links