Variant report

Variant	rs6091796
Chromosome Location	chr20:52580292-52580293
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:732113..733855-chr20:52577889..52580528,2	MCF-7	breast:
2	chr20:52578883..52580609-chr20:52582194..52583717,2	K562	blood:
3	chr20:52578676..52580952-chr20:52822613..52824922,2	MCF-7	breast:
4	chr17:59938997..59940771-chr20:52578844..52581418,2	MCF-7	breast:
5	chr20:52578607..52581315-chr8:144821296..144823256,2	MCF-7	breast:
6	chr17:56708004..56710166-chr20:52580287..52582051,2	MCF-7	breast:
7	chr20:52579682..52581889-chr6:26155321..26157357,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000103266	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000101132	Chromatin interaction
ENSG00000203499	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000136492	Chromatin interaction
ENSG00000161999	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1034843	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs158544	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs208364	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs208366	0.82[YRI][hapmap]
rs208372	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs208373	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs208375	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2276492	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2276508	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2276511	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276512	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299727	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2299733	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2299736	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290389	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs290424	0.83[AMR][1000 genomes]
rs290425	0.83[AMR][1000 genomes]
rs290426	0.83[AMR][1000 genomes]
rs36030456	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs406691	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs459454	0.83[AMR][1000 genomes]
rs4809948	0.93[ASN][1000 genomes]
rs4811488	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6091791	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6091792	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6091793	1.00[YRI][hapmap]
rs6091794	1.00[YRI][hapmap]
rs6091799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6097693	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6097694	1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6097695	0.95[ASN][1000 genomes]
rs6097696	1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs6097697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][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	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
3	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
4	nsv1055549	chr20:52555871-52586281	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52566400-52644800	Weak transcription	Gastric	stomach
2	chr20:52570200-52591800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr20:52570200-52592400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr20:52570800-52590800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr20:52576400-52591400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr20:52577000-52580400	Weak transcription	Fetal Muscle Leg	muscle
7	chr20:52578400-52591200	Weak transcription	HSMMtube	muscle
8	chr20:52578600-52580400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr20:52578600-52592400	Weak transcription	Brain Hippocampus Middle	brain
10	chr20:52578800-52591800	Weak transcription	Brain Anterior Caudate	brain
11	chr20:52578800-52592400	Weak transcription	Brain Substantia Nigra	brain
12	chr20:52580200-52580400	Enhancers	Fetal Stomach	stomach
13	chr20:52580200-52580800	Enhancers	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links