Variant report

Variant	rs12580488
Chromosome Location	chr12:47073570-47073571
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:47058195..47060784-chr12:47071093..47073736,2	MCF-7	breast:
2	chr12:46764550..46767963-chr12:47070058..47075038,6	MCF-7	breast:
3	chr12:46760106..46768771-chr12:47062317..47074742,23	MCF-7	breast:
4	chr12:46774047..46784224-chr12:47066154..47074786,21	MCF-7	breast:
5	chr12:46757591..46759131-chr12:47071589..47074161,2	MCF-7	breast:
6	chr12:46753885..46756732-chr12:47071381..47073599,2	MCF-7	breast:

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

Extended variants
information (count: 140 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs10880980	0.82[EUR][1000 genomes]
rs11183524	0.85[EUR][1000 genomes]
rs11183536	0.85[EUR][1000 genomes]
rs11183539	0.91[EUR][1000 genomes]
rs11183547	0.91[EUR][1000 genomes]
rs11183550	0.91[EUR][1000 genomes]
rs11829502	0.80[EUR][1000 genomes]
rs11830099	0.89[EUR][1000 genomes]
rs11830501	0.89[EUR][1000 genomes]
rs11831177	0.85[AMR][1000 genomes]
rs11831920	0.89[EUR][1000 genomes]
rs11831929	0.89[EUR][1000 genomes]
rs11832316	0.89[EUR][1000 genomes]
rs11833393	0.85[EUR][1000 genomes]
rs11834607	0.85[EUR][1000 genomes]
rs11835517	0.89[EUR][1000 genomes]
rs11835974	0.89[EUR][1000 genomes]
rs11836915	0.82[EUR][1000 genomes]
rs11836940	0.89[EUR][1000 genomes]
rs11837104	0.89[EUR][1000 genomes]
rs12300125	0.85[EUR][1000 genomes]
rs12310635	0.82[EUR][1000 genomes]
rs12578813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12579089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12579348	0.89[EUR][1000 genomes]
rs12579976	0.89[EUR][1000 genomes]
rs12580092	0.86[EUR][1000 genomes]
rs12580356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12581205	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12581311	0.93[EUR][1000 genomes]
rs12581366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12582013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12582034	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12582056	0.91[EUR][1000 genomes]
rs12582305	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12582476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17096991	0.85[EUR][1000 genomes]
rs17096995	0.89[EUR][1000 genomes]
rs17097002	0.85[EUR][1000 genomes]
rs17097009	0.89[EUR][1000 genomes]
rs17097022	0.89[EUR][1000 genomes]
rs17121410	0.85[EUR][1000 genomes]
rs17121412	0.89[EUR][1000 genomes]
rs17594275	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17611638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1946175	0.85[EUR][1000 genomes]
rs2042058	0.96[EUR][1000 genomes]
rs2193663	0.89[EUR][1000 genomes]
rs2216439	0.86[EUR][1000 genomes]
rs235601	0.91[EUR][1000 genomes]
rs235602	0.91[EUR][1000 genomes]
rs235607	0.95[EUR][1000 genomes]
rs235610	0.91[EUR][1000 genomes]
rs235616	0.91[EUR][1000 genomes]
rs235621	0.95[EUR][1000 genomes]
rs235622	0.95[EUR][1000 genomes]
rs235625	0.95[EUR][1000 genomes]
rs235626	0.95[EUR][1000 genomes]
rs235627	0.95[EUR][1000 genomes]
rs2408576	0.89[EUR][1000 genomes]
rs2408577	0.85[EUR][1000 genomes]
rs2430937	0.85[EUR][1000 genomes]
rs2430939	0.85[EUR][1000 genomes]
rs2430940	0.85[EUR][1000 genomes]
rs2430941	0.85[EUR][1000 genomes]
rs2430942	0.85[EUR][1000 genomes]
rs2430943	0.85[EUR][1000 genomes]
rs2430946	0.89[EUR][1000 genomes]
rs2430947	0.86[EUR][1000 genomes]
rs2471581	0.82[EUR][1000 genomes]
rs2471583	0.82[EUR][1000 genomes]
rs2471588	0.85[EUR][1000 genomes]
rs2471594	0.85[EUR][1000 genomes]
rs2471601	0.85[EUR][1000 genomes]
rs2471602	0.85[EUR][1000 genomes]
rs2471605	0.85[EUR][1000 genomes]
rs2471608	0.85[EUR][1000 genomes]
rs2471617	0.85[EUR][1000 genomes]
rs2471618	0.85[EUR][1000 genomes]
rs28768973	0.85[EUR][1000 genomes]
rs2897969	0.86[EUR][1000 genomes]
rs2909411	0.85[EUR][1000 genomes]
rs2960450	0.85[EUR][1000 genomes]
rs34008890	0.95[EUR][1000 genomes]
rs35096979	0.95[EUR][1000 genomes]
rs4073924	0.82[EUR][1000 genomes]
rs4604970	0.89[EUR][1000 genomes]
rs4768741	0.85[EUR][1000 genomes]
rs4768742	0.91[EUR][1000 genomes]
rs4768744	0.93[EUR][1000 genomes]
rs56111534	0.85[EUR][1000 genomes]
rs56152575	0.89[EUR][1000 genomes]
rs56181923	0.89[EUR][1000 genomes]
rs56271434	0.89[EUR][1000 genomes]
rs56399247	0.82[EUR][1000 genomes]
rs57158113	0.82[EUR][1000 genomes]
rs57370043	0.95[EUR][1000 genomes]
rs57658610	0.85[EUR][1000 genomes]
rs58449317	0.89[EUR][1000 genomes]
rs58503088	0.89[EUR][1000 genomes]
rs58561072	0.95[EUR][1000 genomes]
rs58813899	0.89[EUR][1000 genomes]
rs59903937	0.89[EUR][1000 genomes]
rs60049938	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60191997	0.85[EUR][1000 genomes]
rs60432604	0.82[EUR][1000 genomes]
rs60669661	0.89[EUR][1000 genomes]
rs60681792	0.89[EUR][1000 genomes]
rs61072098	0.81[EUR][1000 genomes]
rs61355826	0.85[EUR][1000 genomes]
rs61641663	0.95[EUR][1000 genomes]
rs7138914	0.89[EUR][1000 genomes]
rs7302876	0.80[EUR][1000 genomes]
rs7308386	0.89[EUR][1000 genomes]
rs7310326	0.85[EUR][1000 genomes]
rs7310408	0.93[EUR][1000 genomes]
rs73282109	0.95[EUR][1000 genomes]
rs73290364	0.84[AMR][1000 genomes]
rs73290381	0.82[EUR][1000 genomes]
rs73290402	0.89[EUR][1000 genomes]
rs73291964	0.89[EUR][1000 genomes]
rs73291976	0.89[EUR][1000 genomes]
rs73291980	0.89[EUR][1000 genomes]
rs73292000	0.89[EUR][1000 genomes]
rs73292001	0.85[EUR][1000 genomes]
rs73293911	0.89[EUR][1000 genomes]
rs73293919	0.89[EUR][1000 genomes]
rs74085431	0.85[AMR][1000 genomes]
rs7484802	0.80[EUR][1000 genomes]
rs7488464	0.85[EUR][1000 genomes]
rs765707	0.89[EUR][1000 genomes]
rs766794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7976710	0.89[EUR][1000 genomes]
rs9669050	0.85[EUR][1000 genomes]
rs977069	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	esv3416674	chr12:46988689-47178369	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv558783	chr12:46996632-47144856	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47059600-47076800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:47059800-47076600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr12:47065200-47076200	Weak transcription	Psoas Muscle	Psoas
4	chr12:47070000-47077400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:47071000-47080600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:47071200-47074800	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr12:47071600-47073800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr12:47071600-47074000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr12:47071600-47074000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:47071800-47074000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:47071800-47074200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:47071800-47074400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr12:47071800-47077400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:47072000-47073600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr12:47072000-47073800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr12:47072000-47074000	Weak transcription	HSMM	muscle
17	chr12:47072000-47076000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:47072200-47073600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr12:47072200-47073800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr12:47072200-47074000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:47072400-47074400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:47072600-47074400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:47073000-47074000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:47073000-47074000	Weak transcription	NHEK	skin
25	chr12:47073400-47073800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:47073400-47073800	Weak transcription	HMEC	breast

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