Variant report

Variant	rs58017268
Chromosome Location	chr1:209540074-209540075
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209532175..209545038-chr1:209598052..209610156,35	MCF-7	breast:
2	chr1:209528146..209530754-chr1:209539138..209540797,2	MCF-7	breast:
3	chr1:209527253..209544360-chr1:209599669..209610889,45	MCF-7	breast:
4	chr1:209533760..209536298-chr1:209538566..209540091,2	K562	blood:
5	chr1:209537992..209540217-chr1:209560334..209562277,2	MCF-7	breast:
6	chr1:209538239..209540335-chr1:209559472..209561618,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230937	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1006316	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1006317	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10494921	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1354850	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1354852	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1354853	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1395753	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1507331	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1507336	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17014320	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17014323	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17014337	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17014370	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17014375	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17014395	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17014396	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4844473	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4844807	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4844809	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4844815	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4844820	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4844821	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55684110	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60460414	0.94[ASN][1000 genomes]
rs60534728	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6674793	0.95[ASN][1000 genomes]
rs6681466	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs74155473	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7516757	0.81[ASN][1000 genomes]
rs7516864	0.84[ASN][1000 genomes]
rs7548184	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[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	nsv832481	chr1:209371276-209540333	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv832492	chr1:209383771-209589312	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209526400-209545600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr1:209529800-209547000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:209535400-209543800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:209535800-209542200	Enhancers	NHEK	skin
5	chr1:209535800-209550800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:209536000-209545200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:209536000-209545600	Enhancers	HMEC	breast
8	chr1:209536800-209540200	Weak transcription	Esophagus	oesophagus
9	chr1:209536800-209540800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:209536800-209548600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:209537600-209548600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:209538000-209543200	Weak transcription	Fetal Thymus	thymus
13	chr1:209538000-209547200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:209538600-209542200	Weak transcription	HSMMtube	muscle
15	chr1:209539200-209540200	Weak transcription	Fetal Brain Female	brain
16	chr1:209539400-209540200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:209539600-209540200	Enhancers	Osteobl	bone
18	chr1:209539800-209540200	Enhancers	Muscle Satellite Cultured Cells	--
19	chr1:209539800-209543200	Enhancers	NH-A	brain
20	chr1:209539800-209545600	Enhancers	Fetal Brain Male	brain
21	chr1:209540000-209540400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr1:209540000-209540400	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr1:209540000-209540600	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr1:209540000-209540600	Enhancers	H9 Cell Line	embryonic stem cell
25	chr1:209540000-209541400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:209540000-209542400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:209540000-209542400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:209540000-209542800	Enhancers	Placenta Amnion	Placenta Amnion
29	chr1:209540000-209542800	Enhancers	HSMM	muscle

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