Variant report

Variant	rs10485439
Chromosome Location	chr20:52631250-52631251
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:204256116..204257768-chr20:52629931..52632610,2	MCF-7	breast:
2	chr17:58821413..58822386-chr20:52630813..52631902,3	MCF-7	breast:
3	chr17:58820431..58822124-chr20:52629626..52633490,4	MCF-7	breast:
4	chr17:58820299..58823467-chr20:52630245..52633492,6	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12329598	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs16998697	0.86[YRI][hapmap]
rs16998751	0.81[ASW][hapmap];0.83[LWK][hapmap];0.81[YRI][hapmap]
rs2108453	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2870302	1.00[MEX][hapmap]
rs57324905	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59007419	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6097708	1.00[MEX][hapmap]
rs6097717	1.00[AMR][1000 genomes]
rs6097720	1.00[AMR][1000 genomes]
rs7273075	0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73914470	1.00[AMR][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	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	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

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52566400-52644800	Weak transcription	Gastric	stomach
2	chr20:52618800-52644400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr20:52624000-52633400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr20:52627600-52633200	Weak transcription	Brain Angular Gyrus	brain
5	chr20:52630200-52631400	Enhancers	Brain Anterior Caudate	brain
6	chr20:52630200-52632200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr20:52630600-52631400	Enhancers	Ovary	ovary
8	chr20:52630600-52631400	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr20:52630600-52631600	Enhancers	Brain Hippocampus Middle	brain
10	chr20:52630600-52631600	Enhancers	Fetal Lung	lung
11	chr20:52630600-52632200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr20:52630800-52631400	Enhancers	Stomach Mucosa	stomach
13	chr20:52630800-52633200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr20:52631000-52631400	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr20:52631000-52631400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr20:52631000-52631400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr20:52631000-52631600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr20:52631000-52631600	Enhancers	Adipose Nuclei	Adipose
19	chr20:52631000-52633200	Weak transcription	Brain Substantia Nigra	brain
20	chr20:52631200-52631600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr20:52631200-52631600	Flanking Active TSS	NHDF-Ad	bronchial
22	chr20:52631200-52632200	Enhancers	GM12878-XiMat	blood

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