Variant report

Variant	rs2430939
Chromosome Location	chr12:46939572-46939573
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	chr12:46765109..46767382-chr12:46939505..46942259,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258096	Chromatin interaction
ENSG00000134294	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10880980	0.88[EUR][1000 genomes]
rs11183524	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183536	1.00[EUR][1000 genomes]
rs11183539	0.93[EUR][1000 genomes]
rs11183547	0.93[EUR][1000 genomes]
rs11183550	0.93[EUR][1000 genomes]
rs11829502	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11830099	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11830501	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11831920	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11831929	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11832316	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11833393	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11834607	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11835517	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11835974	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11836915	0.88[EUR][1000 genomes]
rs11836940	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837104	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12300125	1.00[EUR][1000 genomes]
rs12310635	0.84[EUR][1000 genomes]
rs12578813	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12579089	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12579348	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12579976	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12580092	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12580356	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12580488	0.85[EUR][1000 genomes]
rs12581311	0.88[EUR][1000 genomes]
rs12581366	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12582013	0.85[EUR][1000 genomes]
rs12582056	0.93[EUR][1000 genomes]
rs12582476	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17096991	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17096995	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17097002	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17097009	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17097022	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17121410	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17121412	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17594275	0.85[EUR][1000 genomes]
rs17611638	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1946175	1.00[EUR][1000 genomes]
rs2042058	0.88[EUR][1000 genomes]
rs2193662	0.91[EUR][1000 genomes]
rs2193663	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2216439	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235601	0.93[EUR][1000 genomes]
rs235602	0.93[EUR][1000 genomes]
rs235607	0.90[EUR][1000 genomes]
rs235610	0.93[EUR][1000 genomes]
rs235616	0.86[EUR][1000 genomes]
rs235621	0.90[EUR][1000 genomes]
rs235622	0.90[EUR][1000 genomes]
rs235625	0.90[EUR][1000 genomes]
rs235626	0.90[EUR][1000 genomes]
rs235627	0.90[EUR][1000 genomes]
rs2408576	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408577	1.00[EUR][1000 genomes]
rs2430937	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2430940	1.00[EUR][1000 genomes]
rs2430941	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2430942	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2430943	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2430946	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2430947	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471581	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2471583	0.88[EUR][1000 genomes]
rs2471588	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2471594	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471601	1.00[EUR][1000 genomes]
rs2471602	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471605	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471608	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471617	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471618	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28768973	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2897969	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2909411	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2960450	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34008890	0.90[EUR][1000 genomes]
rs35096979	0.90[EUR][1000 genomes]
rs4073924	0.88[EUR][1000 genomes]
rs4604970	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768125	0.93[EUR][1000 genomes]
rs4768741	0.81[EUR][1000 genomes]
rs4768742	0.87[EUR][1000 genomes]
rs4768744	0.88[EUR][1000 genomes]
rs56111534	0.87[EUR][1000 genomes]
rs56152575	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56181923	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56271434	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56399247	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57158113	0.88[EUR][1000 genomes]
rs57370043	0.90[EUR][1000 genomes]
rs57658610	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58449317	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58503088	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58561072	0.90[EUR][1000 genomes]
rs58813899	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59903937	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60191997	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60432604	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60669661	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60681792	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61072098	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61355826	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61641663	0.90[EUR][1000 genomes]
rs7138914	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302876	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7308386	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310326	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7310408	0.88[EUR][1000 genomes]
rs73282109	0.90[EUR][1000 genomes]
rs73290381	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73290402	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73291964	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73291976	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73291980	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73292000	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73292001	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73293911	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73293919	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7484802	0.83[EUR][1000 genomes]
rs7488464	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765707	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs766794	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7976710	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9669050	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs977069	0.86[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	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
5	esv3402095	chr12:46937340-46983181	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46925200-46940600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:46925400-46940200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:46925600-46940000	Weak transcription	NHEK	skin
4	chr12:46925800-46940200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:46928400-46948600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr12:46930600-46940000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr12:46930800-46940200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:46933200-46940200	Weak transcription	GM12878-XiMat	blood
9	chr12:46933400-46940400	Weak transcription	HepG2	liver
10	chr12:46933800-46939600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr12:46938600-46940000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
12	chr12:46938600-46941800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:46939000-46939800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:46939000-46940600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:46939400-46940000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr12:46939400-46940000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:46939400-46940000	Weak transcription	Dnd41	blood
18	chr12:46939400-46940400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell

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