Variant report

Variant	rs58880008
Chromosome Location	chr5:106922963-106922964
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	chr5:106922846..106925376-chr5:107006745..107008300,2	MCF-7	breast:
2	chr5:106921384..106923070-chr5:106934624..106936760,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10043284	1.00[ASN][1000 genomes]
rs10043302	1.00[ASN][1000 genomes]
rs10044934	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515374	1.00[ASN][1000 genomes]
rs12110095	1.00[ASN][1000 genomes]
rs12514246	1.00[ASN][1000 genomes]
rs12515248	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12519552	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12519591	1.00[ASN][1000 genomes]
rs12520660	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522223	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17160227	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58882389	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6881619	1.00[ASN][1000 genomes]
rs6888194	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6895165	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs755966	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7726649	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7732162	1.00[ASN][1000 genomes]
rs9328006	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs957662	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	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
2	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
3	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:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106913600-106928800	Weak transcription	Right Ventricle	heart
2	chr5:106913800-106924000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr5:106914000-106924800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:106914200-106924000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:106914800-106928200	Weak transcription	Left Ventricle	heart
6	chr5:106915200-106929800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:106915600-106928200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:106917000-106929200	Weak transcription	HMEC	breast
9	chr5:106917400-106924200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:106917400-106928000	Weak transcription	HSMMtube	muscle
11	chr5:106917600-106923600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:106917600-106928200	Weak transcription	A549	lung
13	chr5:106917800-106928600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr5:106919600-106924000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr5:106919800-106928200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:106920200-106924000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:106920800-106928400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:106922000-106924600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr5:106922200-106923400	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links