Variant report

Variant	rs4768777
Chromosome Location	chr12:47558207-47558208
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	chr12:47557715..47560552-chr12:47561242..47563669,2	MCF-7	breast:
2	chr12:47556322..47559512-chr12:47571534..47574931,3	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10785658	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs10785660	0.89[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10785661	0.83[CEU][hapmap];0.85[CHB][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10881051	0.83[CEU][hapmap]
rs10881056	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10881057	0.86[EUR][1000 genomes]
rs10881058	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11183755	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs11183769	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11183774	0.90[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs12371765	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12578367	0.83[CEU][hapmap]
rs12578995	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12579796	0.83[CEU][hapmap]
rs12830116	0.82[CEU][hapmap]
rs1357933	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1357935	0.95[CEU][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1404812	0.83[CEU][hapmap]
rs1404819	0.83[CEU][hapmap]
rs1525444	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs1525453	0.82[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1830054	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1880600	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1917658	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1949864	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs2091294	0.83[CEU][hapmap]
rs2408714	0.90[CEU][hapmap]
rs4768141	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4768775	0.83[CEU][hapmap]
rs55651541	0.85[EUR][1000 genomes]
rs6582696	0.90[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7135951	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7136496	0.84[AMR][1000 genomes]
rs7295263	0.82[CEU][hapmap]
rs7297792	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7311824	0.83[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7958186	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs7958922	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7963822	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs7974123	0.83[EUR][1000 genomes]
rs9634260	0.90[CEU][hapmap];0.87[EUR][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	nsv469368	chr12:47374908-47675680	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv558784	chr12:47374908-47675680	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv832399	chr12:47502910-47689601	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2751100	chr12:47541390-47746157	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47536000-47578000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:47536200-47564200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:47541600-47558400	Weak transcription	NHEK	skin
4	chr12:47550400-47558400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr12:47550400-47560000	Weak transcription	Adipose Nuclei	Adipose
6	chr12:47550400-47562200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:47550600-47558400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:47550600-47558400	Weak transcription	Ovary	ovary
9	chr12:47550600-47558400	Weak transcription	Right Atrium	heart
10	chr12:47550600-47571800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr12:47550600-47582400	Weak transcription	Aorta	Aorta
12	chr12:47550800-47560000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr12:47550800-47570000	Weak transcription	Colon Smooth Muscle	Colon
14	chr12:47550800-47570200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr12:47551200-47583600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:47551400-47567200	Weak transcription	Spleen	Spleen
17	chr12:47554600-47558400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:47554800-47579600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr12:47555000-47559800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr12:47555000-47565800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr12:47555000-47576400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:47556200-47558600	Strong transcription	Primary B cells from cord blood	blood
23	chr12:47556600-47558400	Weak transcription	Left Ventricle	heart
24	chr12:47556600-47560000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr12:47556800-47560200	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr12:47556800-47570400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr12:47557000-47559200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:47557000-47559200	Enhancers	NHDF-Ad	bronchial
29	chr12:47557400-47558600	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr12:47557400-47564600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr12:47557600-47558600	Enhancers	Stomach Mucosa	stomach
32	chr12:47557600-47558800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:47557600-47558800	Enhancers	Pancreas	Pancrea
34	chr12:47557600-47558800	Enhancers	NHLF	lung
35	chr12:47557600-47559000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:47557600-47559400	Strong transcription	Primary T cells from cord blood	blood
37	chr12:47557800-47558600	Weak transcription	K562	blood
38	chr12:47557800-47558800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr12:47557800-47558800	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr12:47557800-47560400	Enhancers	A549	lung
41	chr12:47557800-47581600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr12:47558000-47558600	Enhancers	Liver	Liver
43	chr12:47558000-47559000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:47558000-47559000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:47558000-47559000	Enhancers	Osteobl	bone
46	chr12:47558200-47558600	Enhancers	Gastric	stomach
47	chr12:47558200-47558800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:47558200-47558800	Enhancers	Lung	lung
49	chr12:47558200-47559400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr12:47558200-47560200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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