Variant report

Variant	rs12489858
Chromosome Location	chr3:111464460-111464461
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111459238..111460946-chr3:111462346..111465281,2	MCF-7	breast:

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10934105	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10934108	0.83[EUR][1000 genomes]
rs12495513	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][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	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv829676	chr3:111464087-111619200	Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111456200-111465600	Weak transcription	Primary T cells from cord blood	blood
2	chr3:111458000-111467000	Weak transcription	Right Ventricle	heart
3	chr3:111458600-111467200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:111458800-111464800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:111458800-111466800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:111459000-111466400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:111459000-111466400	Weak transcription	NHDF-Ad	bronchial
8	chr3:111459000-111466600	Weak transcription	Stomach Mucosa	stomach
9	chr3:111459200-111464600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:111459200-111466400	Weak transcription	Gastric	stomach
11	chr3:111459200-111466600	Weak transcription	Osteobl	bone
12	chr3:111459400-111465600	Weak transcription	HepG2	liver
13	chr3:111460200-111464800	Weak transcription	A549	lung
14	chr3:111460400-111464600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:111460400-111464600	Weak transcription	HMEC	breast
16	chr3:111460600-111464600	Weak transcription	NHEK	skin
17	chr3:111462400-111466800	Weak transcription	Liver	Liver
18	chr3:111462600-111467000	Weak transcription	Fetal Kidney	kidney
19	chr3:111462600-111468000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:111462600-111468000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr3:111463000-111469600	Weak transcription	Adipose Nuclei	Adipose
22	chr3:111463800-111468200	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:111464000-111467000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:111464200-111465200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:111464200-111465400	Enhancers	Hela-S3	cervix
26	chr3:111464400-111464800	Enhancers	Placenta	Placenta
27	chr3:111464400-111465200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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