Variant report

Variant	rs28497391
Chromosome Location	chr5:112585389-112585390
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	chr5:112585167..112587277-chr5:112587981..112591044,3	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10037836	1.00[AMR][1000 genomes]
rs10037845	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10042401	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10056104	1.00[AMR][1000 genomes]
rs10477489	1.00[AMR][1000 genomes]
rs10478116	1.00[AMR][1000 genomes]
rs11958613	1.00[AMR][1000 genomes]
rs12110055	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13357188	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13358281	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17135568	0.89[AMR][1000 genomes]
rs17135570	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs28439752	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28462299	1.00[AMR][1000 genomes]
rs2860051	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28711712	1.00[AMR][1000 genomes]
rs55889115	1.00[AMR][1000 genomes]
rs57727389	0.89[AMR][1000 genomes]
rs59032550	1.00[AMR][1000 genomes]
rs61560548	1.00[AMR][1000 genomes]
rs73781507	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73781509	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73781510	1.00[AMR][1000 genomes]
rs73781511	1.00[AMR][1000 genomes]
rs73781512	1.00[AMR][1000 genomes]
rs7718459	1.00[AMR][1000 genomes]
rs7720189	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7736171	0.90[AFR][1000 genomes];1.00[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	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882718	chr5:112519471-112674376	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv882719	chr5:112568212-112706511	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112557200-112585800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:112572400-112590400	Weak transcription	Liver	Liver
3	chr5:112572600-112585800	Weak transcription	Pancreas	Pancrea
4	chr5:112575400-112585400	Weak transcription	Colon Smooth Muscle	Colon
5	chr5:112579600-112585400	Weak transcription	Esophagus	oesophagus
6	chr5:112579600-112587000	Weak transcription	Aorta	Aorta
7	chr5:112580600-112597400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:112581400-112590800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:112582200-112585400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr5:112582200-112586400	Weak transcription	HMEC	breast
11	chr5:112582400-112585400	Weak transcription	Fetal Kidney	kidney
12	chr5:112582600-112585600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr5:112582600-112585800	Weak transcription	Fetal Lung	lung
14	chr5:112582800-112585400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr5:112582800-112585400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr5:112582800-112585400	Weak transcription	Stomach Mucosa	stomach
17	chr5:112582800-112585600	Weak transcription	HSMM	muscle
18	chr5:112582800-112585800	Weak transcription	HSMMtube	muscle
19	chr5:112582800-112586000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:112582800-112586000	Weak transcription	Placenta	Placenta
21	chr5:112582800-112586400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr5:112582800-112586400	Weak transcription	NHEK	skin
23	chr5:112582800-112601000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr5:112583000-112585400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr5:112583000-112585400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr5:112583000-112585400	Weak transcription	NHDF-Ad	bronchial
27	chr5:112583000-112585600	Weak transcription	Adipose Nuclei	Adipose
28	chr5:112583000-112586200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr5:112583000-112586400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr5:112583000-112604600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr5:112583200-112585800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr5:112583200-112586400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr5:112583200-112587000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr5:112583600-112585800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr5:112583600-112586000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr5:112583600-112599800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr5:112583800-112585400	Weak transcription	Psoas Muscle	Psoas
38	chr5:112583800-112586000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:112583800-112587000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr5:112583800-112588000	Enhancers	Fetal Heart	heart
41	chr5:112584400-112585800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:112584400-112586400	Enhancers	Stomach Smooth Muscle	stomach
43	chr5:112584400-112587400	Enhancers	NH-A	brain
44	chr5:112584400-112587400	Enhancers	Osteobl	bone
45	chr5:112584800-112586000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr5:112584800-112586200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr5:112584800-112586800	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr5:112585000-112585800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:112585000-112585800	Enhancers	Rectal Smooth Muscle	rectum
50	chr5:112585000-112587000	Enhancers	Skeletal Muscle Male	skeletal muscle

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