Variant report

Variant	rs12828052
Chromosome Location	chr12:45612971-45612972
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:45611569..45613822-chr12:45799872..45802476,2	MCF-7	breast:
2	chr12:45609724..45611735-chr12:45612584..45615895,4	MCF-7	breast:
3	chr12:45612938..45614519-chr12:45750771..45753564,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134297	Chromatin interaction
ENSG00000177119	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10437984	0.85[EUR][1000 genomes]
rs10459293	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10459294	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10492284	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10785556	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10785557	0.85[EUR][1000 genomes]
rs10880757	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10880758	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10880760	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10880761	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10880762	0.85[EUR][1000 genomes]
rs10880763	0.85[EUR][1000 genomes]
rs10880764	0.85[EUR][1000 genomes]
rs11182898	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11182899	0.89[ASN][1000 genomes]
rs11182903	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11182904	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11182912	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11182913	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11182915	0.81[AFR][1000 genomes]
rs11182916	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11182917	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11182918	0.85[EUR][1000 genomes]
rs11182919	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11182921	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11182922	0.85[EUR][1000 genomes]
rs11182923	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11182927	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11182931	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11182935	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11182936	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11182938	0.85[EUR][1000 genomes]
rs11182939	0.85[EUR][1000 genomes]
rs11182940	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11182941	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11182942	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11182943	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11182944	0.85[EUR][1000 genomes]
rs11182946	0.85[EUR][1000 genomes]
rs11182947	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11182949	0.83[EUR][1000 genomes]
rs11182953	0.86[ASN][1000 genomes]
rs11182954	0.86[ASN][1000 genomes]
rs11182955	0.86[ASN][1000 genomes]
rs11561532	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11610233	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11611509	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11612203	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11612233	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11615850	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12226944	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12227678	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12228733	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12230322	0.85[EUR][1000 genomes]
rs12299174	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12320168	0.85[EUR][1000 genomes]
rs12320437	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12322087	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12814332	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12815115	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12815334	0.86[ASN][1000 genomes]
rs12815723	0.86[ASN][1000 genomes]
rs12818421	0.83[ASN][1000 genomes]
rs12822746	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17095551	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17095557	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2052602	0.85[EUR][1000 genomes]
rs2052603	0.83[EUR][1000 genomes]
rs2408184	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2408185	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34024171	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35054776	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35588430	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35660715	0.85[EUR][1000 genomes]
rs3759077	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3759080	0.85[EUR][1000 genomes]
rs3759081	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3759082	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3782131	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57560057	0.86[ASN][1000 genomes]
rs57797434	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61923810	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61923825	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61923830	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7138983	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7954282	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7963038	0.85[EUR][1000 genomes]
rs7963057	0.85[EUR][1000 genomes]
rs9739519	0.85[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050923	chr12:45581310-45808289	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45608400-45613400	Active TSS	Stomach Smooth Muscle	stomach
2	chr12:45608800-45613400	Active TSS	Aorta	Aorta
3	chr12:45610800-45613400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:45611000-45613600	Weak transcription	Spleen	Spleen
5	chr12:45611000-45614400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr12:45611000-45617600	Weak transcription	Gastric	stomach
7	chr12:45611000-45624800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:45611200-45613000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr12:45611200-45613000	Weak transcription	Brain Anterior Caudate	brain
10	chr12:45611200-45613000	Weak transcription	Lung	lung
11	chr12:45611200-45613200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:45611200-45613200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:45611200-45613600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:45611200-45613800	Enhancers	Primary T cells fromperipheralblood	blood
15	chr12:45611200-45614600	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr12:45611200-45614800	Weak transcription	Pancreas	Pancrea
17	chr12:45611200-45628000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:45611400-45614000	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr12:45611400-45614000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr12:45611400-45614800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr12:45611400-45615800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr12:45611600-45613400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr12:45611600-45613600	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr12:45611600-45614200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr12:45611600-45629400	Weak transcription	Fetal Muscle Trunk	muscle
26	chr12:45611800-45613000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:45611800-45613000	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr12:45611800-45613200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr12:45611800-45614400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr12:45611800-45615200	Enhancers	Fetal Lung	lung
31	chr12:45611800-45615600	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr12:45611800-45615600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:45611800-45624800	Weak transcription	HSMM	muscle
34	chr12:45612000-45613000	Enhancers	Fetal Muscle Leg	muscle
35	chr12:45612000-45613000	Enhancers	HSMMtube	muscle
36	chr12:45612000-45613200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:45612000-45613400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:45612000-45613600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr12:45612000-45614000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:45612000-45614000	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr12:45612000-45614000	Enhancers	Left Ventricle	heart
42	chr12:45612000-45614400	Enhancers	Fetal Heart	heart
43	chr12:45612000-45614600	Enhancers	Hela-S3	cervix
44	chr12:45612000-45614800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr12:45612000-45615600	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr12:45612000-45617600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr12:45612200-45613400	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr12:45612200-45613400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr12:45612200-45613600	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr12:45612200-45613800	Enhancers	Monocytes-CD14+_RO01746	blood

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