Variant report

Variant	rs235626
Chromosome Location	chr12:47062441-47062442
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:47060948..47064525-chr12:47070342..47072791,3	MCF-7	breast:
2	chr12:47060607..47062700-chr12:47063813..47065440,2	MCF-7	breast:
3	chr12:46760106..46768771-chr12:47062317..47074742,23	MCF-7	breast:
4	chr12:47061845..47064516-chr12:47065041..47068020,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134294	Chromatin interaction
ENSG00000258096	Chromatin interaction

Extended variants
information (count: 143 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs10785631	1.00[CEU][hapmap]
rs10880975	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs10880976	1.00[CEU][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs10880977	1.00[CEU][hapmap];0.84[CHD][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs11183524	0.90[EUR][1000 genomes]
rs11183536	0.90[EUR][1000 genomes]
rs11183539	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11183547	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11183550	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11829502	1.00[CEU][hapmap]
rs11830099	0.84[EUR][1000 genomes]
rs11830501	0.84[EUR][1000 genomes]
rs11831177	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs11831920	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11831929	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11832316	0.84[EUR][1000 genomes]
rs11833393	0.90[EUR][1000 genomes]
rs11834607	0.90[EUR][1000 genomes]
rs11835517	0.84[EUR][1000 genomes]
rs11835974	0.84[EUR][1000 genomes]
rs11836915	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs11836940	1.00[CEU][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs11837104	0.84[EUR][1000 genomes]
rs12300125	1.00[CEU][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs12310635	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12320420	0.86[AMR][1000 genomes]
rs12578813	0.91[EUR][1000 genomes]
rs12579089	0.91[EUR][1000 genomes]
rs12579348	0.84[EUR][1000 genomes]
rs12579976	0.84[EUR][1000 genomes]
rs12580092	0.91[EUR][1000 genomes]
rs12580121	1.00[CEU][hapmap]
rs12580356	0.91[EUR][1000 genomes]
rs12580488	0.95[EUR][1000 genomes]
rs12581205	0.89[EUR][1000 genomes]
rs12581311	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12581366	0.91[EUR][1000 genomes]
rs12582013	0.95[EUR][1000 genomes]
rs12582056	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12582305	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs12582476	0.91[EUR][1000 genomes]
rs17096991	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs17096995	1.00[CEU][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs17097002	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs17097009	0.84[EUR][1000 genomes]
rs17097022	1.00[CEU][hapmap];0.84[GIH][hapmap];0.84[EUR][1000 genomes]
rs17121410	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs17121412	1.00[CEU][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs17594275	0.95[EUR][1000 genomes]
rs17611638	0.91[EUR][1000 genomes]
rs1946175	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2042058	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2193662	0.81[EUR][1000 genomes]
rs2193663	0.84[EUR][1000 genomes]
rs2216439	0.81[EUR][1000 genomes]
rs235600	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs235601	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs235602	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs235607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235610	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs235616	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs235617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs235621	1.00[CEU][hapmap];0.92[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs235622	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs235625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs235627	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2408576	0.84[EUR][1000 genomes]
rs2408577	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2430937	0.90[EUR][1000 genomes]
rs2430939	0.90[EUR][1000 genomes]
rs2430940	1.00[CEU][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2430941	0.90[EUR][1000 genomes]
rs2430942	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2430943	0.90[EUR][1000 genomes]
rs2430946	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2430947	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2471583	1.00[CEU][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap]
rs2471588	0.90[EUR][1000 genomes]
rs2471594	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2471601	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2471602	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2471605	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs2471608	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2471617	0.90[EUR][1000 genomes]
rs2471618	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs28768973	0.90[EUR][1000 genomes]
rs2897969	0.81[EUR][1000 genomes]
rs2909411	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2960450	0.90[EUR][1000 genomes]
rs34008890	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35096979	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4604970	0.84[EUR][1000 genomes]
rs4768125	0.83[EUR][1000 genomes]
rs4768740	0.86[MEX][hapmap]
rs4768741	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768742	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4768744	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56111534	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56152575	0.84[EUR][1000 genomes]
rs56181923	0.84[EUR][1000 genomes]
rs56271434	0.84[EUR][1000 genomes]
rs57370043	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57658610	0.90[EUR][1000 genomes]
rs58449317	0.84[EUR][1000 genomes]
rs58503088	0.84[EUR][1000 genomes]
rs58561072	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58813899	0.84[EUR][1000 genomes]
rs59903937	0.84[EUR][1000 genomes]
rs60191997	0.90[EUR][1000 genomes]
rs60669661	0.84[EUR][1000 genomes]
rs60681792	0.84[EUR][1000 genomes]
rs61072098	0.86[EUR][1000 genomes]
rs61355826	0.90[EUR][1000 genomes]
rs61641663	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6582666	1.00[CEU][hapmap]
rs7138914	0.84[EUR][1000 genomes]
rs7295471	1.00[CEU][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs7308386	0.84[EUR][1000 genomes]
rs7310326	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7310408	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7310614	0.86[MEX][hapmap]
rs73282109	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73290402	0.84[EUR][1000 genomes]
rs73291964	0.84[EUR][1000 genomes]
rs73291976	0.84[EUR][1000 genomes]
rs73291980	0.84[EUR][1000 genomes]
rs73292000	0.84[EUR][1000 genomes]
rs73292001	0.90[EUR][1000 genomes]
rs73293911	0.84[EUR][1000 genomes]
rs73293919	0.84[EUR][1000 genomes]
rs7484802	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7488464	0.90[EUR][1000 genomes]
rs765707	0.84[EUR][1000 genomes]
rs766794	0.91[EUR][1000 genomes]
rs7976710	0.84[EUR][1000 genomes]
rs9669050	0.90[EUR][1000 genomes]
rs977069	1.00[CEU][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv1844378	chr12:47028797-47072016	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	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:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47046400-47069800	Weak transcription	Pancreas	Pancrea
2	chr12:47054000-47068400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr12:47054000-47071400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:47056000-47069000	Weak transcription	Esophagus	oesophagus
5	chr12:47059000-47065600	Weak transcription	Primary B cells from cord blood	blood
6	chr12:47059600-47063600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:47059600-47069200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:47059600-47069800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr12:47059600-47076800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr12:47059800-47064800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr12:47059800-47068800	Weak transcription	NHLF	lung
12	chr12:47059800-47076600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr12:47060000-47064200	Weak transcription	Psoas Muscle	Psoas
14	chr12:47060000-47068000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:47060000-47068000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:47060200-47063800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:47061000-47062600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:47061400-47067600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:47061600-47067600	Weak transcription	NHEK	skin
20	chr12:47061600-47068000	Weak transcription	NHDF-Ad	bronchial
21	chr12:47061800-47063200	Weak transcription	HMEC	breast
22	chr12:47061800-47065000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
23	chr12:47062000-47062800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
24	chr12:47062000-47063000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
25	chr12:47062000-47063000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:47062000-47064200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
27	chr12:47062000-47067800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr12:47062200-47068000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:47062400-47063200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
30	chr12:47062400-47063200	Enhancers	H9 Cell Line	embryonic stem cell
31	chr12:47062400-47063400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell

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