Variant report

Variant	rs57628489
Chromosome Location	chr3:111460129-111460130
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	chr3:111459238..111460946-chr3:111462346..111465281,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10934104	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11709591	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12638437	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1398749	1.00[ASN][1000 genomes]
rs1398752	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1398755	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1513332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1513333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1513334	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35840064	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35894167	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4234402	1.00[ASN][1000 genomes]
rs4682055	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682062	1.00[ASN][1000 genomes]
rs4682297	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60556634	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6438002	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6768082	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6791600	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6800228	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7427989	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7620801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636559	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7640416	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7642808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643067	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7644696	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7648126	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7650348	1.00[ASN][1000 genomes]
rs7651391	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7653881	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv591290	chr3:111427455-111462570	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111451600-111460400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:111452800-111460400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:111454800-111460400	Enhancers	Fetal Heart	heart
4	chr3:111454800-111464400	Weak transcription	Placenta	Placenta
5	chr3:111455000-111461000	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr3:111455800-111461000	Enhancers	Rectal Smooth Muscle	rectum
7	chr3:111456200-111465600	Weak transcription	Primary T cells from cord blood	blood
8	chr3:111457400-111460200	Weak transcription	Fetal Kidney	kidney
9	chr3:111458000-111467000	Weak transcription	Right Ventricle	heart
10	chr3:111458600-111460400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:111458600-111462200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:111458600-111464400	Weak transcription	Psoas Muscle	Psoas
13	chr3:111458600-111467200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:111458800-111461800	Weak transcription	Adipose Nuclei	Adipose
15	chr3:111458800-111464800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:111458800-111466800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:111459000-111460200	Enhancers	A549	lung
18	chr3:111459000-111460400	Enhancers	HMEC	breast
19	chr3:111459000-111462200	Weak transcription	Colon Smooth Muscle	Colon
20	chr3:111459000-111466400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:111459000-111466400	Weak transcription	NHDF-Ad	bronchial
22	chr3:111459000-111466600	Weak transcription	Stomach Mucosa	stomach
23	chr3:111459200-111460200	Weak transcription	Left Ventricle	heart
24	chr3:111459200-111460600	Enhancers	NHEK	skin
25	chr3:111459200-111462200	Weak transcription	Pancreas	Pancrea
26	chr3:111459200-111464600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr3:111459200-111466400	Weak transcription	Gastric	stomach
28	chr3:111459200-111466600	Weak transcription	Osteobl	bone
29	chr3:111459400-111465600	Weak transcription	HepG2	liver
30	chr3:111459800-111464200	Weak transcription	Hela-S3	cervix
31	chr3:111460000-111460200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:111460000-111460200	Enhancers	Liver	Liver
33	chr3:111460000-111460200	Enhancers	Fetal Muscle Leg	muscle
34	chr3:111460000-111460400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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