Variant report

Variant	rs4445718
Chromosome Location	chr12:28354222-28354223
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	chr12:28341800..28343671-chr12:28353988..28355644,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247934	Chromatin interaction
ENSG00000123106	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10492051	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1180008	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17433716	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17434682	0.81[AMR][1000 genomes]
rs17434731	0.81[AMR][1000 genomes]
rs17434809	0.81[AMR][1000 genomes]
rs17512249	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17525767	0.81[AMR][1000 genomes]
rs1796415	0.82[EUR][1000 genomes]
rs28360439	0.92[AMR][1000 genomes]
rs28969463	0.82[EUR][1000 genomes]
rs3850517	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4083358	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41416850	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55728984	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55817936	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55846109	0.84[EUR][1000 genomes]
rs55847639	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56017922	0.81[AMR][1000 genomes]
rs56156773	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56159890	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7312738	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73214189	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73214193	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73214200	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73214202	0.99[EUR][1000 genomes]
rs73216105	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73216108	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73216109	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73216110	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73216131	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73218207	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73218210	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73218221	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7959194	0.81[AMR][1000 genomes]
rs7973360	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv557864	chr12:28052194-28430102	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1048513	chr12:28060407-28424109	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv557876	chr12:28114816-28725104	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:28344400-28355400	Weak transcription	Ovary	ovary
2	chr12:28344800-28355400	Weak transcription	Left Ventricle	heart
3	chr12:28344800-28355400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:28344800-28362400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:28344800-28363800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:28345000-28355600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr12:28345000-28362200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr12:28345000-28368800	Weak transcription	Brain Hippocampus Middle	brain
9	chr12:28345000-28369600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr12:28345200-28355400	Weak transcription	Brain Anterior Caudate	brain
11	chr12:28345200-28355400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:28345400-28359000	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr12:28345400-28370400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:28346000-28355800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:28346000-28362400	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr12:28346000-28369800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:28346200-28355400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr12:28347800-28358600	Weak transcription	Primary B cells from cord blood	blood
19	chr12:28347800-28362400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:28347800-28363400	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr12:28347800-28363800	Weak transcription	Fetal Stomach	stomach
22	chr12:28347800-28364000	Weak transcription	Thymus	Thymus
23	chr12:28348000-28355200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:28348000-28362000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:28348000-28366800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:28348000-28367800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr12:28348200-28385400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:28348400-28362000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:28349600-28355400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr12:28349600-28355400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr12:28351200-28355400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr12:28351200-28358800	Weak transcription	Brain Substantia Nigra	brain
33	chr12:28352000-28354800	Weak transcription	Pancreas	Pancrea
34	chr12:28352000-28362400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:28352400-28362400	Weak transcription	Fetal Thymus	thymus
36	chr12:28353000-28362200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:28353200-28354800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:28353200-28355200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:28353200-28360000	Weak transcription	Primary T cells from cord blood	blood
40	chr12:28353200-28362600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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