Variant report

Variant	rs28112
Chromosome Location	chr5:106815980-106815981
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:106808580..106812777-chr5:106814056..106818233,4	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs25740	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs25964	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs25965	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs26235	0.82[EUR][1000 genomes]
rs26241	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26243	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs26244	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs27929	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28024	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28208	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28764	0.82[EUR][1000 genomes]
rs29543	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030118	chr5:106006097-106847949	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1034276	chr5:106461538-106944163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv537851	chr5:106461538-106944163	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv34018	chr5:106720912-107110506	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106805600-106822600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:106806000-106825600	Weak transcription	Aorta	Aorta
3	chr5:106806200-106822200	Weak transcription	HSMM	muscle
4	chr5:106808400-106837800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:106808600-106822600	Weak transcription	Gastric	stomach
6	chr5:106808800-106822800	Weak transcription	Left Ventricle	heart
7	chr5:106809000-106822800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:106810400-106817800	Weak transcription	Right Atrium	heart
9	chr5:106811200-106816800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr5:106811400-106817200	Weak transcription	Small Intestine	intestine
11	chr5:106811600-106819200	Weak transcription	Fetal Lung	lung
12	chr5:106812000-106816000	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr5:106812200-106816200	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr5:106813000-106816800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:106813000-106817200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr5:106813000-106819200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr5:106813200-106816600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr5:106813200-106821400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr5:106814000-106818400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:106814000-106819000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:106814000-106821600	Weak transcription	Right Ventricle	heart
22	chr5:106814200-106819000	Weak transcription	GM12878-XiMat	blood
23	chr5:106814200-106819000	Weak transcription	NHDF-Ad	bronchial
24	chr5:106814400-106817000	Weak transcription	Fetal Heart	heart
25	chr5:106814400-106817600	Weak transcription	Stomach Mucosa	stomach
26	chr5:106814400-106819400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr5:106814400-106819400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr5:106814400-106821000	Weak transcription	HMEC	breast
29	chr5:106814600-106816000	Weak transcription	A549	lung
30	chr5:106814600-106816200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:106814600-106818800	Weak transcription	Fetal Kidney	kidney
32	chr5:106815000-106821600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:106815000-106823000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr5:106815200-106822800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr5:106815400-106816400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr5:106815400-106818000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:106815400-106818800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr5:106815400-106818800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr5:106815400-106819400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr5:106815400-106820800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr5:106815400-106821400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr5:106815600-106818200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr5:106815600-106819000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr5:106815600-106819800	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr5:106815600-106822600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr5:106815800-106818800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr5:106815800-106821000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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