Variant report

Variant	rs28485564
Chromosome Location	chr3:56167236-56167237
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	chr3:56164542..56167534-chr3:56237841..56240212,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1023970	0.85[ASN][1000 genomes]
rs1466178	0.80[ASN][1000 genomes]
rs1519030	0.95[ASN][1000 genomes]
rs17056469	0.95[ASN][1000 genomes]
rs17056493	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28397662	0.95[ASN][1000 genomes]
rs28471370	0.85[ASN][1000 genomes]
rs28496913	0.95[ASN][1000 genomes]
rs28689027	0.85[ASN][1000 genomes]
rs56141852	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6788505	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73078492	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73078494	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73091055	0.95[ASN][1000 genomes]
rs9311597	0.95[ASN][1000 genomes]
rs9811952	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820348	0.85[ASN][1000 genomes]
rs9824306	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9830503	0.95[ASN][1000 genomes]
rs9833446	0.85[ASN][1000 genomes]
rs9844377	0.95[ASN][1000 genomes]
rs9853630	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862097	0.95[ASN][1000 genomes]
rs9873343	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9876574	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013063	chr3:55835413-56173713	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1009709	chr3:56000827-56294945	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr3:56157800-56175400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:56160000-56170600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:56163000-56171400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:56164800-56168000	Enhancers	NHLF	lung
5	chr3:56164800-56168200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr3:56165200-56168800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:56165200-56170600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:56165400-56168200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:56165400-56168200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:56165400-56168800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:56165400-56168800	Enhancers	HSMM	muscle
12	chr3:56165600-56168000	Enhancers	HMEC	breast
13	chr3:56165600-56168200	Enhancers	NHEK	skin
14	chr3:56165600-56168200	Enhancers	Osteobl	bone
15	chr3:56165600-56168600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:56165800-56168200	Enhancers	HUVEC	blood vessel
17	chr3:56166200-56167400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:56166200-56168000	Weak transcription	Brain Germinal Matrix	brain
19	chr3:56166400-56167600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:56166400-56167600	Weak transcription	HSMMtube	muscle
21	chr3:56166400-56168200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:56166400-56168200	Enhancers	NH-A	brain
23	chr3:56166400-56168600	Enhancers	NHDF-Ad	bronchial
24	chr3:56166400-56168800	Enhancers	Muscle Satellite Cultured Cells	--
25	chr3:56166400-56170400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr3:56166400-56171000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:56166400-56173600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:56166600-56167600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:56166600-56170200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:56166600-56170200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr3:56166600-56171200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:56166800-56169400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:56167000-56167600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:56167200-56167800	Enhancers	A549	lung

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