Variant report

Variant	rs10880975
Chromosome Location	chr12:46886543-46886544
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:28)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:28 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46735506..46737094-chr12:46885760..46887551,2	MCF-7	breast:
2	chr12:46885059..46886744-chr12:46888077..46890213,2	K562	blood:
3	chr12:46659275..46663300-chr12:46885422..46888676,6	MCF-7	breast:
4	chr12:46885974..46889693-chr12:46900997..46904051,5	MCF-7	breast:
5	chr12:46849293..46850290-chr12:46885983..46886935,2	MCF-7	breast:
6	chr12:46876888..46879463-chr12:46886100..46887929,2	MCF-7	breast:
7	chr12:46885920..46888548-chr12:47063563..47066194,2	MCF-7	breast:
8	chr12:46661057..46663892-chr12:46886146..46888578,3	MCF-7	breast:
9	chr12:46770827..46772736-chr12:46884583..46887256,2	MCF-7	breast:
10	chr12:46884995..46887012-chr12:47057652..47060520,3	MCF-7	breast:
11	chr12:46844776..46847490-chr12:46885701..46888274,3	MCF-7	breast:
12	chr12:46885590..46888355-chr12:47169213..47171245,2	MCF-7	breast:
13	chr12:46759647..46768800-chr12:46881212..46889672,42	MCF-7	breast:
14	chr12:46775174..46780982-chr12:46884437..46889035,12	MCF-7	breast:
15	chr12:46886050..46886867-chr12:46902675..46903414,2	MCF-7	breast:
16	chr12:46886016..46887722-chr12:47054283..47056459,2	MCF-7	breast:
17	chr12:46752026..46753720-chr12:46885951..46888111,2	K562	blood:
18	chr12:46881119..46884848-chr12:46886427..46890898,4	K562	blood:
19	chr12:46850310..46852807-chr12:46885920..46888687,3	MCF-7	breast:
20	chr12:46755348..46759433-chr12:46884546..46888564,7	MCF-7	breast:
21	chr12:46748037..46750227-chr12:46886535..46888305,2	MCF-7	breast:
22	chr12:46867596..46869336-chr12:46885001..46888174,3	MCF-7	breast:
23	chr12:46761219..46768367-chr12:46884244..46889425,20	MCF-7	breast:
24	chr12:46856551..46858642-chr12:46884704..46886633,2	MCF-7	breast:
25	chr12:46885465..46887733-chr12:47068809..47070995,2	MCF-7	breast:
26	chr12:46885416..46887111-chr12:47052344..47054021,2	MCF-7	breast:
27	chr12:46773608..46782926-chr12:46881237..46891957,39	MCF-7	breast:
28	chr12:46850397..46853199-chr12:46885229..46888347,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257496	Chromatin interaction
ENSG00000258096	Chromatin interaction
ENSG00000257261	Chromatin interaction
ENSG00000111371	Chromatin interaction
ENSG00000134294	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10785631	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10880976	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10880977	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10880980	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11183464	1.00[CEU][hapmap]
rs11183497	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11183507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11183527	0.86[YRI][hapmap]
rs11183536	0.84[AMR][1000 genomes]
rs11504523	1.00[EUR][1000 genomes]
rs11829502	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11830099	0.82[EUR][1000 genomes]
rs11830501	0.82[EUR][1000 genomes]
rs11831177	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11831920	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11831929	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11832316	0.82[EUR][1000 genomes]
rs11835517	0.82[EUR][1000 genomes]
rs11835974	0.82[EUR][1000 genomes]
rs11836915	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11836940	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11837104	0.82[EUR][1000 genomes]
rs12300125	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes]
rs12303824	0.81[EUR][1000 genomes]
rs12305921	1.00[CEU][hapmap]
rs12579348	0.82[EUR][1000 genomes]
rs12579976	0.82[EUR][1000 genomes]
rs12580121	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12582056	1.00[CEU][hapmap]
rs17096991	1.00[CEU][hapmap]
rs17096995	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17097002	1.00[CEU][hapmap]
rs17097009	0.82[EUR][1000 genomes]
rs17097022	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17121410	1.00[CEU][hapmap]
rs17121412	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1946175	0.90[AMR][1000 genomes]
rs2042058	1.00[CEU][hapmap]
rs2193662	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2193663	0.82[EUR][1000 genomes]
rs235607	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs235617	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs235621	1.00[CEU][hapmap]
rs235622	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs235626	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs2408576	0.82[EUR][1000 genomes]
rs2408577	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2430940	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2430942	1.00[CEU][hapmap]
rs2430946	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2430947	1.00[CEU][hapmap]
rs2471581	0.85[EUR][1000 genomes]
rs2471583	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2471594	1.00[CEU][hapmap]
rs2471601	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2471602	1.00[CEU][hapmap]
rs2471605	1.00[CEU][hapmap]
rs2471608	1.00[CEU][hapmap]
rs2471618	1.00[CEU][hapmap]
rs2909411	1.00[CEU][hapmap]
rs4073924	0.85[EUR][1000 genomes]
rs4604970	0.82[EUR][1000 genomes]
rs4768125	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4768731	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4768735	0.85[YRI][hapmap]
rs4768741	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs4768744	1.00[CEU][hapmap]
rs56152575	0.82[EUR][1000 genomes]
rs56181923	0.82[EUR][1000 genomes]
rs56271434	0.82[EUR][1000 genomes]
rs56399247	0.85[EUR][1000 genomes]
rs57158113	0.85[EUR][1000 genomes]
rs57439008	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58449317	0.82[EUR][1000 genomes]
rs58503088	0.82[EUR][1000 genomes]
rs58813899	0.82[EUR][1000 genomes]
rs59521025	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59903937	0.82[EUR][1000 genomes]
rs60432604	0.85[EUR][1000 genomes]
rs60669661	0.82[EUR][1000 genomes]
rs60681792	0.82[EUR][1000 genomes]
rs6582666	1.00[CEU][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7138914	0.82[EUR][1000 genomes]
rs7295471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7302876	0.84[EUR][1000 genomes]
rs7308386	0.82[EUR][1000 genomes]
rs7310326	1.00[CEU][hapmap]
rs73290364	0.96[EUR][1000 genomes]
rs73290381	0.85[EUR][1000 genomes]
rs73290402	0.82[EUR][1000 genomes]
rs73291964	0.82[EUR][1000 genomes]
rs73291976	0.82[EUR][1000 genomes]
rs73291980	0.82[EUR][1000 genomes]
rs73292000	0.82[EUR][1000 genomes]
rs73293911	0.82[EUR][1000 genomes]
rs73293919	0.82[EUR][1000 genomes]
rs74085431	1.00[EUR][1000 genomes]
rs765707	0.82[EUR][1000 genomes]
rs7976710	0.82[EUR][1000 genomes]
rs977069	1.00[CEU][hapmap]
rs9783500	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][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:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46868600-46889200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:46871200-46887800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:46878000-46887400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr12:46878200-46886600	Enhancers	HepG2	liver
5	chr12:46878200-46887000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:46880600-46888600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:46881800-46888000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr12:46882400-46888600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:46882600-46889600	Weak transcription	Primary B cells from cord blood	blood
10	chr12:46882800-46894200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr12:46883000-46886800	Enhancers	Ovary	ovary
12	chr12:46883000-46888800	Enhancers	HMEC	breast
13	chr12:46883200-46886600	Enhancers	NHLF	lung
14	chr12:46883200-46886800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:46883200-46887800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:46883200-46889000	Enhancers	NHEK	skin
17	chr12:46883400-46886800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:46883400-46887600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:46883400-46887800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:46883400-46888800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:46883800-46886600	Enhancers	Muscle Satellite Cultured Cells	--
22	chr12:46883800-46887400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr12:46884000-46886800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr12:46884000-46888200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr12:46884200-46888000	Weak transcription	Fetal Stomach	stomach
26	chr12:46884200-46888600	Weak transcription	Pancreas	Pancrea
27	chr12:46884400-46887400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr12:46884400-46889000	Enhancers	Osteobl	bone
29	chr12:46884600-46887800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr12:46884800-46887600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr12:46884800-46887800	Weak transcription	Colon Smooth Muscle	Colon
32	chr12:46884800-46888600	Weak transcription	Left Ventricle	heart
33	chr12:46885000-46887800	Weak transcription	Adipose Nuclei	Adipose
34	chr12:46885400-46886600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr12:46885400-46886600	Enhancers	Right Atrium	heart
36	chr12:46885400-46889000	Enhancers	Liver	Liver
37	chr12:46885600-46888800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:46885800-46887000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr12:46885800-46887000	Enhancers	Stomach Mucosa	stomach
40	chr12:46885800-46887200	Enhancers	Placenta	Placenta
41	chr12:46885800-46887600	Flanking Active TSS	A549	lung
42	chr12:46885800-46888800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:46886000-46886600	Enhancers	H9 Cell Line	embryonic stem cell
44	chr12:46886000-46886600	Enhancers	Right Ventricle	heart
45	chr12:46886000-46886800	Enhancers	Psoas Muscle	Psoas
46	chr12:46886000-46887800	Enhancers	HSMMtube	muscle
47	chr12:46886000-46888600	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr12:46886000-46888600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:46886000-46889000	Enhancers	Fetal Lung	lung
50	chr12:46886000-46889000	Enhancers	HSMM	muscle

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