Variant report

Variant	rs12299174
Chromosome Location	chr12:45594693-45594694
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	chr12:45593253..45599943-chr12:45607385..45612735,9	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ANO6-3	chr12:45594600-45595334	NONHSAT027824

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	0.81[EUR][1000 genomes]
rs10459293	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10459294	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10492284	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10785556	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10785557	0.81[EUR][1000 genomes]
rs10880757	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10880758	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10880760	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10880761	0.87[AMR][1000 genomes]
rs10880762	0.81[EUR][1000 genomes]
rs10880763	0.81[EUR][1000 genomes]
rs10880764	0.81[EUR][1000 genomes]
rs11182898	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11182899	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182903	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182904	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182905	0.91[EUR][1000 genomes]
rs11182908	0.91[EUR][1000 genomes]
rs11182912	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11182913	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11182916	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11182917	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11182918	0.81[EUR][1000 genomes]
rs11182919	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11182921	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11182922	0.81[EUR][1000 genomes]
rs11182923	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11182927	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11182931	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11182935	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11182936	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11182938	0.81[EUR][1000 genomes]
rs11182939	0.81[EUR][1000 genomes]
rs11182940	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11182941	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11182942	0.87[ASN][1000 genomes]
rs11182943	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11182944	0.81[EUR][1000 genomes]
rs11182946	0.81[EUR][1000 genomes]
rs11182947	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11182953	0.82[ASN][1000 genomes]
rs11182954	0.82[ASN][1000 genomes]
rs11182955	0.82[ASN][1000 genomes]
rs11561532	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11610233	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611509	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11612203	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11612233	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11615850	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12226944	0.91[ASN][1000 genomes]
rs12227678	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12228733	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12230322	0.81[EUR][1000 genomes]
rs12231753	0.91[EUR][1000 genomes]
rs12320168	0.81[EUR][1000 genomes]
rs12320437	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12322087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12814332	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12815115	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12815334	0.82[ASN][1000 genomes]
rs12815723	0.82[ASN][1000 genomes]
rs12822746	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12828052	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17095551	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17095557	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2052602	0.81[EUR][1000 genomes]
rs2408184	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2408185	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34024171	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35054776	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35588430	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35660715	0.81[EUR][1000 genomes]
rs3759077	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3759080	0.81[EUR][1000 genomes]
rs3759081	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3759082	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3782131	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57560057	0.82[ASN][1000 genomes]
rs57797434	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61923804	0.86[EUR][1000 genomes]
rs61923810	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61923825	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61923830	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7138983	0.90[AMR][1000 genomes]
rs7954282	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7963038	0.81[EUR][1000 genomes]
rs7963057	0.81[EUR][1000 genomes]
rs9739519	0.81[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:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45579400-45599200	Weak transcription	Primary B cells from cord blood	blood
2	chr12:45586600-45602400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:45592200-45599400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr12:45593000-45594800	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr12:45593000-45595200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr12:45593000-45595400	Enhancers	Fetal Intestine Large	intestine
7	chr12:45593000-45595600	Enhancers	HepG2	liver
8	chr12:45593200-45595200	Enhancers	Placenta Amnion	Placenta Amnion
9	chr12:45593400-45594800	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr12:45593400-45595000	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr12:45593400-45600000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:45593600-45595000	Flanking Active TSS	Dnd41	blood
13	chr12:45593600-45595200	Enhancers	Fetal Thymus	thymus
14	chr12:45593600-45595400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr12:45593800-45594800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr12:45593800-45594800	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr12:45593800-45594800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:45593800-45594800	Active TSS	Stomach Smooth Muscle	stomach
19	chr12:45593800-45595000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:45593800-45595000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:45593800-45595200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:45593800-45595200	Flanking Active TSS	Liver	Liver
23	chr12:45593800-45595200	Enhancers	Small Intestine	intestine
24	chr12:45593800-45595800	Enhancers	Fetal Intestine Small	intestine
25	chr12:45594000-45594800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:45594000-45594800	Enhancers	Fetal Lung	lung
27	chr12:45594000-45594800	Enhancers	Placenta	Placenta
28	chr12:45594000-45594800	Enhancers	NHLF	lung
29	chr12:45594000-45595200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr12:45594000-45595200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr12:45594200-45594800	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr12:45594200-45594800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr12:45594200-45594800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr12:45594200-45594800	Enhancers	GM12878-XiMat	blood
35	chr12:45594200-45595000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:45594200-45595200	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr12:45594200-45595400	Enhancers	Primary hematopoietic stem cells	blood
38	chr12:45594400-45594800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:45594400-45594800	Enhancers	Primary B cells from peripheral blood	blood
40	chr12:45594400-45594800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr12:45594400-45595000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr12:45594400-45595200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr12:45594600-45594800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr12:45594600-45594800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:45594600-45594800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr12:45594600-45594800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr12:45594600-45594800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:45594600-45594800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr12:45594600-45594800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr12:45594600-45594800	Flanking Active TSS	Adipose Nuclei	Adipose

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