Variant report

Variant	rs25980
Chromosome Location	chr5:106821777-106821778
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	chr5:106807029..106809976-chr5:106820820..106823619,3	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs152562	0.81[EUR][1000 genomes]
rs25966	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs25969	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs25972	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs25979	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs25981	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs25982	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs25996	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs25997	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs26236	0.86[EUR][1000 genomes]
rs26240	0.86[EUR][1000 genomes]
rs27853	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28001	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs31717	0.93[EUR][1000 genomes]
rs32013	0.83[EUR][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:51 , 50 per page) page: 1 2

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	chr5:106815000-106823000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr5:106815200-106822800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:106815600-106822600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr5:106816200-106822800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr5:106817200-106822400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr5:106817400-106821800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr5:106817600-106825000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr5:106817600-106829800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr5:106818400-106821800	Weak transcription	Stomach Mucosa	stomach
17	chr5:106818400-106825000	Weak transcription	Right Atrium	heart
18	chr5:106818600-106822000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr5:106818800-106821800	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr5:106819000-106821800	Enhancers	GM12878-XiMat	blood
21	chr5:106819800-106823800	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr5:106820000-106822200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr5:106820200-106822600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr5:106820400-106822400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:106820400-106822800	Weak transcription	Fetal Heart	heart
26	chr5:106820600-106822000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:106820600-106822200	Weak transcription	NHDF-Ad	bronchial
28	chr5:106820600-106838200	Weak transcription	Fetal Brain Male	brain
29	chr5:106820800-106822600	Enhancers	A549	lung
30	chr5:106821000-106822600	Enhancers	HMEC	breast
31	chr5:106821000-106823200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr5:106821200-106823600	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr5:106821400-106822800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr5:106821400-106822800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr5:106821400-106822800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr5:106821400-106823200	Enhancers	Primary T cells fromperipheralblood	blood
37	chr5:106821400-106823200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr5:106821400-106823400	Enhancers	Dnd41	blood
39	chr5:106821600-106821800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:106821600-106821800	Enhancers	Right Ventricle	heart
41	chr5:106821600-106822600	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr5:106821600-106822600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr5:106821600-106822600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr5:106821600-106822600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr5:106821600-106823000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr5:106821600-106823000	Enhancers	Primary T cells from cord blood	blood
47	chr5:106821600-106823000	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr5:106821600-106823200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr5:106821600-106823200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr5:106821600-106823200	Enhancers	NHEK	skin

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