Variant report

Variant	rs11831177
Chromosome Location	chr12:46911235-46911236
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	chr12:46764120..46766517-chr12:46908748..46911657,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258096	Chromatin interaction
ENSG00000134294	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10785631	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10880975	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10880976	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10880977	1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10880980	0.85[EUR][1000 genomes]
rs11183464	1.00[CEU][hapmap];0.85[TSI][hapmap]
rs11183497	1.00[CEU][hapmap];0.83[CHD][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11183507	1.00[EUR][1000 genomes]
rs11504523	1.00[EUR][1000 genomes]
rs11829502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11830099	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11830501	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11831920	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11831929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11832316	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11835517	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11835974	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11836915	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11836940	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11837104	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12300125	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs12303824	0.81[EUR][1000 genomes]
rs12305921	1.00[CEU][hapmap];0.83[CHD][hapmap];0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs12578813	0.85[AMR][1000 genomes]
rs12579089	0.85[AMR][1000 genomes]
rs12579348	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12579976	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12580121	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[EUR][1000 genomes]
rs12580356	0.85[AMR][1000 genomes]
rs12580488	0.85[AMR][1000 genomes]
rs12581205	0.85[AMR][1000 genomes]
rs12581366	0.85[AMR][1000 genomes]
rs12582013	0.85[AMR][1000 genomes]
rs12582056	1.00[CEU][hapmap]
rs12582476	0.85[AMR][1000 genomes]
rs17096991	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.84[YRI][hapmap];0.81[ASN][1000 genomes]
rs17096995	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17097002	1.00[CEU][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes]
rs17097009	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17097022	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17121410	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs17121412	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17594275	0.85[AMR][1000 genomes]
rs17611638	0.85[AMR][1000 genomes]
rs2042058	1.00[CEU][hapmap]
rs2193663	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2216439	0.81[AMR][1000 genomes]
rs235607	1.00[CEU][hapmap]
rs235617	1.00[CEU][hapmap]
rs235621	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs235622	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs235626	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs2408576	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2430940	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs2430942	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs2430946	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2430947	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes]
rs2471581	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2471583	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2471588	0.81[ASN][1000 genomes]
rs2471594	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2471602	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2471605	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.80[YRI][hapmap]
rs2471608	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs2471618	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.80[YRI][hapmap]
rs2897969	0.86[AMR][1000 genomes]
rs2909411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4073924	0.85[EUR][1000 genomes]
rs4604970	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4768731	0.96[EUR][1000 genomes]
rs4768741	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs4768744	1.00[CEU][hapmap]
rs56152575	0.82[EUR][1000 genomes]
rs56181923	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56271434	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56399247	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57158113	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57439008	1.00[EUR][1000 genomes]
rs58449317	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58503088	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58813899	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59521025	1.00[EUR][1000 genomes]
rs59903937	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60432604	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60669661	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60681792	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6582666	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7138914	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7295471	1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7302876	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7308386	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7310326	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs73290364	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73290381	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73290402	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73291964	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73291976	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73291980	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73292000	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73293911	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73293919	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs74085431	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765707	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs766794	0.85[AMR][1000 genomes]
rs7976710	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs977069	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs9783500	1.00[EUR][1000 genomes]
rs9971651	1.00[CEU][hapmap]

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	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
2	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46893400-46911600	Weak transcription	Osteobl	bone
2	chr12:46903400-46917800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:46905400-46915800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr12:46906200-46912400	Weak transcription	Fetal Kidney	kidney
5	chr12:46907400-46911600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:46908000-46917400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr12:46908400-46914400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:46908600-46911400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:46909200-46912400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:46909400-46911600	Genic enhancers	NHEK	skin
11	chr12:46909400-46916000	Enhancers	Ovary	ovary
12	chr12:46909600-46912600	Enhancers	HepG2	liver
13	chr12:46909600-46916400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:46910000-46915800	Weak transcription	HUVEC	blood vessel
15	chr12:46910200-46915000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:46910400-46911600	Enhancers	Primary B cells from cord blood	blood
17	chr12:46910400-46911800	Enhancers	Primary B cells from peripheral blood	blood
18	chr12:46910400-46912200	Enhancers	Primary T cells from cord blood	blood
19	chr12:46910400-46913000	Flanking Active TSS	GM12878-XiMat	blood
20	chr12:46910400-46913600	Enhancers	Fetal Stomach	stomach
21	chr12:46910400-46914800	Weak transcription	Fetal Muscle Leg	muscle
22	chr12:46910600-46911400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr12:46910600-46911400	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr12:46910600-46911600	Enhancers	Fetal Thymus	thymus
25	chr12:46910600-46911600	Strong transcription	HSMM	muscle
26	chr12:46910600-46911800	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr12:46910600-46911800	Enhancers	Duodenum Mucosa	Duodenum
28	chr12:46910600-46912200	Enhancers	Stomach Smooth Muscle	stomach
29	chr12:46910600-46912400	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr12:46910600-46914600	Weak transcription	Fetal Heart	heart
31	chr12:46910800-46911400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr12:46910800-46911400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr12:46910800-46911600	Enhancers	Dnd41	blood
34	chr12:46910800-46911800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:46910800-46911800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:46910800-46912000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr12:46910800-46912000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr12:46910800-46913600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr12:46910800-46914800	Weak transcription	Placenta	Placenta
40	chr12:46910800-46915600	Weak transcription	A549	lung
41	chr12:46910800-46918000	Weak transcription	Psoas Muscle	Psoas
42	chr12:46910800-46920000	Enhancers	Fetal Lung	lung
43	chr12:46911000-46911400	Enhancers	HMEC	breast
44	chr12:46911000-46911800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr12:46911000-46912200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:46911000-46912200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr12:46911000-46912200	Enhancers	Small Intestine	intestine
48	chr12:46911000-46914800	Weak transcription	Spleen	Spleen
49	chr12:46911000-46915000	Weak transcription	Right Ventricle	heart
50	chr12:46911000-46917000	Weak transcription	Fetal Muscle Trunk	muscle

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