Variant report

Variant	rs58332880
Chromosome Location	chr15:39956063-39956064
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:39926150..39927736-chr15:39954644..39957261,2	MCF-7	breast:
2	chr15:39870612..39877795-chr15:39952369..39962860,18	MCF-7	breast:
3	chr15:39913171..39923947-chr15:39954798..39966806,32	MCF-7	breast:
4	chr15:39876509..39878370-chr15:39955744..39957926,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1004739	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1004740	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1004741	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11633974	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11638500	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856294	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11857927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969445	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16969460	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16969495	0.82[ASN][1000 genomes]
rs16969637	0.83[AFR][1000 genomes]
rs2008623	0.88[AFR][1000 genomes]
rs2087132	0.83[AFR][1000 genomes]
rs2411312	0.83[EUR][1000 genomes]
rs2412409	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2412410	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2412411	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34275067	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35754803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784390	0.80[EUR][1000 genomes]
rs4476147	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56722485	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57969006	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60884629	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62004766	0.83[AFR][1000 genomes]
rs72725045	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39938000-39957600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:39949400-39956200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:39950200-39957200	Weak transcription	HSMM	muscle
4	chr15:39950400-39957200	Weak transcription	HSMMtube	muscle
5	chr15:39950800-39957800	Weak transcription	HUVEC	blood vessel
6	chr15:39954400-39956400	Weak transcription	Fetal Kidney	kidney
7	chr15:39954400-39958200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr15:39954400-39958200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr15:39954400-39958200	Weak transcription	NH-A	brain
10	chr15:39954400-39959000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr15:39954600-39958200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr15:39954800-39956200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr15:39955600-39956200	Enhancers	Fetal Lung	lung
14	chr15:39955600-39956400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr15:39955600-39959800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:39955800-39956200	Enhancers	Hela-S3	cervix
17	chr15:39955800-39956400	Enhancers	NHLF	lung
18	chr15:39955800-39957600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr15:39955800-39958400	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr15:39955800-39960200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:39955800-39960200	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr15:39956000-39956200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr15:39956000-39958800	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr15:39956000-39958800	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr15:39956000-39960200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links