Variant report

Variant	rs4712872
Chromosome Location	chr6:24990786-24990787
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24720596..24722709-chr6:24989331..24991417,2	K562	blood:
2	chr6:24858123..24860977-chr6:24989589..24991591,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112308	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10946739	0.95[EUR][1000 genomes]
rs10946740	0.81[EUR][1000 genomes]
rs12192232	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12194111	0.88[CEU][hapmap];0.88[CHD][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes]
rs12205717	0.91[EUR][1000 genomes]
rs1410686	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1410687	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2149452	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2209932	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2894032	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4712870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712871	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712876	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62401116	0.95[EUR][1000 genomes]
rs6456640	0.81[EUR][1000 genomes]
rs6456641	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6935286	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7740315	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7753740	0.81[EUR][1000 genomes]
rs7765689	0.82[EUR][1000 genomes]
rs7765852	0.82[EUR][1000 genomes]
rs7768143	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9295639	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9295640	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295641	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9358815	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9358816	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9366591	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9393600	0.96[CEU][hapmap];0.82[JPT][hapmap];0.81[YRI][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1019504	chr6:24869174-24994758	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv883482	chr6:24926730-25035920	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS 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	43 gene(s)	inside rSNPs	diseases
6	nsv1030634	chr6:24938277-25040161	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24981200-24991800	Weak transcription	Thymus	Thymus
2	chr6:24981800-24992000	Weak transcription	Gastric	stomach
3	chr6:24982200-24991800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:24982400-24991800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:24984200-24995200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:24986000-24996600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:24986400-24992000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr6:24986400-24992800	Enhancers	Primary B cells from peripheral blood	blood
9	chr6:24986400-24995200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:24986400-24995400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:24986600-24991000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:24986600-24992000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:24986600-24996600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:24987600-25000200	Weak transcription	Lung	lung
15	chr6:24987800-24990800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr6:24988000-24991200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:24988200-24991800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr6:24988400-24992000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr6:24989000-24990800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr6:24989000-24992000	Weak transcription	Dnd41	blood
21	chr6:24989200-24991200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:24989800-24991800	Enhancers	Primary B cells from cord blood	blood
23	chr6:24990000-24991800	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr6:24990000-24992800	Enhancers	Primary T cells fromperipheralblood	blood
25	chr6:24990200-24991200	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr6:24990200-24992200	Enhancers	Stomach Mucosa	stomach
27	chr6:24990400-24991000	Enhancers	Primary T cells from cord blood	blood
28	chr6:24990400-24991000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:24990400-24991600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr6:24990400-24991800	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr6:24990400-24991800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr6:24990400-24991800	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr6:24990400-24992600	Enhancers	Fetal Heart	heart
34	chr6:24990400-24992600	Enhancers	Hela-S3	cervix
35	chr6:24990400-24992600	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr6:24990400-24992800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr6:24990400-24993800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr6:24990600-24990800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr6:24990600-24991000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:24990600-24991600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:24990600-24991600	Weak transcription	GM12878-XiMat	blood
42	chr6:24990600-24992200	Enhancers	HSMM	muscle
43	chr6:24990600-24992600	Enhancers	Primary hematopoietic stem cells	blood
44	chr6:24990600-24992600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr6:24990600-24992800	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr6:24990600-24993000	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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