Variant report

Variant	rs10880977
Chromosome Location	chr12:46901429-46901430
allele	A/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46885974..46889693-chr12:46900997..46904051,5	MCF-7	breast:
2	chr12:46759096..46760660-chr12:46901323..46903298,2	MCF-7	breast:
3	chr12:46845917..46847463-chr12:46900708..46902756,2	MCF-7	breast:
4	chr12:46897498..46899915-chr12:46900125..46903070,2	MCF-7	breast:
5	chr12:46780011..46782697-chr12:46900139..46902948,3	MCF-7	breast:
6	chr12:46835195..46837772-chr12:46901174..46903724,2	MCF-7	breast:
7	chr12:46894664..46897223-chr12:46898115..46901985,3	MCF-7	breast:
8	chr12:46762419..46768660-chr12:46899477..46903825,13	MCF-7	breast:
9	chr12:46895836..46897418-chr12:46900604..46903513,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000257496	Chromatin interaction
ENSG00000258096	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[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10880975	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]
rs10880976	1.00[CEU][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10880980	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11183464	1.00[CEU][hapmap];0.85[TSI][hapmap]
rs11183497	1.00[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs11183507	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11183536	0.87[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];0.84[GIH][hapmap];1.00[TSI][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];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs11836940	1.00[CEU][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs11837104	0.82[EUR][1000 genomes]
rs12300125	1.00[CEU][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes]
rs12301825	0.87[MEX][hapmap]
rs12303824	0.81[EUR][1000 genomes]
rs12305921	1.00[CEU][hapmap];0.85[TSI][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];0.87[TSI][hapmap]
rs17096995	1.00[CEU][hapmap];1.00[TSI][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];0.87[TSI][hapmap]
rs17121412	1.00[CEU][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs1946175	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2042058	1.00[CEU][hapmap]
rs2193662	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2193663	0.82[EUR][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];0.84[CHD][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs235626	1.00[CEU][hapmap];0.84[CHD][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs2408576	0.82[EUR][1000 genomes]
rs2408577	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2430940	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.87[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	0.86[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2471594	1.00[CEU][hapmap]
rs2471601	0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2471602	1.00[CEU][hapmap]
rs2471605	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs2471608	1.00[CEU][hapmap]
rs2471618	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs2909411	1.00[CEU][hapmap]
rs4073924	0.85[EUR][1000 genomes]
rs4604970	0.82[EUR][1000 genomes]
rs4768124	0.82[MEX][hapmap]
rs4768125	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4768731	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4768741	1.00[CEU][hapmap];0.84[CHD][hapmap];0.82[MEX][hapmap];0.87[TSI][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	0.85[AFR][1000 genomes];1.00[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	1.00[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7138914	0.82[EUR][1000 genomes]
rs7295471	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.87[TSI][hapmap]
rs9783500	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46888600-46909200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:46893400-46911600	Weak transcription	Osteobl	bone
3	chr12:46899600-46901600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr12:46900000-46901800	Weak transcription	NH-A	brain
5	chr12:46900600-46901600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:46900800-46901800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr12:46901000-46901600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:46901200-46902400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:46901200-46902800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:46901200-46903200	Enhancers	Hela-S3	cervix
11	chr12:46901200-46903600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr12:46901400-46901600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:46901400-46901600	Flanking Active TSS	NHEK	skin
14	chr12:46901400-46902400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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