Variant report

Variant	rs12832396
Chromosome Location	chr12:121581681-121581682
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	chr12:121575022..121577625-chr12:121581601..121583531,2	MCF-7	breast:

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs12810503	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12813980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12814235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12816966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12817169	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12819523	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12819930	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12820593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12824585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12830584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718153	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17432871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17434640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17525809	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs208302	0.94[ASN][1000 genomes]
rs2260138	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2393752	0.94[ASN][1000 genomes]
rs2393753	0.83[ASN][1000 genomes]
rs2393754	0.85[ASN][1000 genomes]
rs28360446	1.00[AFR][1000 genomes]
rs28969465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28969469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34185850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34325588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34449339	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs34480856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34572498	1.00[ASN][1000 genomes]
rs34805626	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs34811727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34934130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35018823	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35076950	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35158421	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35237790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35362296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35455367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35579189	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35605477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35607692	0.87[AMR][1000 genomes]
rs35760636	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35869834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35940217	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs36133237	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs494986	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs513113	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs514109	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56098349	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs583187	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs585847	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs588130	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs588510	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs588573	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs599785	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs601636	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs603505	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs603891	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs618201	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs657172	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66570654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66811517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs670541	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs675718	0.94[ASN][1000 genomes]
rs676632	0.94[ASN][1000 genomes]
rs67691679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67739439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67881993	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs67898046	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71454676	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71454679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71454680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73214191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73214199	1.00[AMR][1000 genomes]
rs73216114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73218241	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs934353	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs934354	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs934355	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	esv2758318	chr12:121415845-121584813	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv2759917	chr12:121415845-121584813	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv832531	chr12:121440495-121604232	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv560454	chr12:121457073-121745742	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv1054878	chr12:121519880-121761800	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv455729	chr12:121525591-121761800	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv560455	chr12:121525591-121761800	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv899563	chr12:121543011-121600529	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1050519	chr12:121552964-121756420	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121571400-121582800	Weak transcription	Lung	lung
2	chr12:121571400-121594000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:121571800-121582400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:121571800-121623200	Weak transcription	Colonic Mucosa	Colon
5	chr12:121572000-121582800	Weak transcription	Primary B cells from cord blood	blood
6	chr12:121572200-121582200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:121572200-121582400	Weak transcription	NHLF	lung
8	chr12:121572200-121583000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr12:121572200-121599800	Weak transcription	Colon Smooth Muscle	Colon
10	chr12:121572600-121592600	Weak transcription	Liver	Liver
11	chr12:121572800-121581800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:121572800-121601600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr12:121576400-121582400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr12:121576600-121581800	Weak transcription	HepG2	liver
15	chr12:121576600-121592400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr12:121577000-121593400	Weak transcription	Primary T cells from cord blood	blood
17	chr12:121577400-121582000	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr12:121578200-121585200	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr12:121578200-121592400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr12:121580200-121581800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr12:121580200-121582400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:121580200-121582600	Weak transcription	Brain Anterior Caudate	brain
23	chr12:121580400-121581800	Weak transcription	Brain Hippocampus Middle	brain
24	chr12:121580400-121581800	Weak transcription	Brain Substantia Nigra	brain
25	chr12:121580400-121592000	Weak transcription	Ovary	ovary
26	chr12:121580400-121592400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr12:121580800-121582400	Weak transcription	Brain Angular Gyrus	brain
28	chr12:121580800-121584000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:121581000-121583200	Enhancers	Placenta	Placenta
30	chr12:121581000-121584000	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr12:121581200-121582200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:121581400-121582000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:121581400-121583200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:121581400-121583200	Enhancers	Primary B cells from peripheral blood	blood
35	chr12:121581400-121583200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr12:121581400-121583400	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr12:121581400-121583800	Enhancers	K562	blood
38	chr12:121581600-121582200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:121581600-121582200	Flanking Active TSS	GM12878-XiMat	blood
40	chr12:121581600-121582600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:121581600-121582600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:121581600-121582800	Enhancers	Hela-S3	cervix
43	chr12:121581600-121583200	Enhancers	Dnd41	blood
44	chr12:121581600-121583200	Enhancers	NHEK	skin
45	chr12:121581600-121583800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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