Variant report

Variant	rs1572707
Chromosome Location	chr20:23230122-23230123
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23226825..23230641-chr20:23238537..23241083,3	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1099456	0.85[ASN][1000 genomes]
rs11696272	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs1338942	0.93[CEU][hapmap];0.91[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1338944	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1416399	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1538446	0.91[CHB][hapmap];0.96[JPT][hapmap];0.86[ASN][1000 genomes]
rs1856470	0.90[ASN][1000 genomes]
rs2024897	0.86[ASN][1000 genomes]
rs4813485	0.81[ASN][1000 genomes]
rs4813486	0.81[ASN][1000 genomes]
rs6036338	0.91[ASN][1000 genomes]
rs6048590	0.91[CHB][hapmap];0.96[JPT][hapmap];0.88[ASN][1000 genomes]
rs6048591	0.88[ASN][1000 genomes]
rs6048592	0.91[ASN][1000 genomes]
rs6048595	0.91[CHB][hapmap];0.96[JPT][hapmap];0.91[ASN][1000 genomes]
rs6048612	0.94[ASN][1000 genomes]
rs6048615	0.96[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6048618	0.97[ASN][1000 genomes]
rs6048619	0.97[ASN][1000 genomes]
rs6076038	0.86[ASN][1000 genomes]
rs6076039	0.90[ASN][1000 genomes]
rs6076041	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6083030	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6083032	0.86[ASN][1000 genomes]
rs6083033	0.87[ASN][1000 genomes]
rs6083036	0.87[ASN][1000 genomes]
rs6083038	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6083042	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6083043	0.91[CHB][hapmap];0.96[JPT][hapmap];0.91[ASN][1000 genomes]
rs6132577	0.88[ASN][1000 genomes]
rs6132579	0.83[ASN][1000 genomes]
rs62206882	0.85[ASN][1000 genomes]
rs750652	0.85[ASN][1000 genomes]
rs8118328	0.86[ASN][1000 genomes]
rs844924	0.84[ASN][1000 genomes]
rs844929	0.84[ASN][1000 genomes]
rs844930	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs844932	0.91[CHB][hapmap];0.96[JPT][hapmap];0.85[ASN][1000 genomes]
rs844934	0.91[CHB][hapmap];0.96[JPT][hapmap];0.85[ASN][1000 genomes]
rs844936	0.85[ASN][1000 genomes]
rs844937	0.91[CHB][hapmap];0.96[JPT][hapmap];0.85[ASN][1000 genomes]
rs844938	0.85[ASN][1000 genomes]
rs844939	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs844940	0.85[ASN][1000 genomes]
rs844941	0.86[ASN][1000 genomes]
rs844942	0.91[CHB][hapmap];0.96[JPT][hapmap]
rs867909	0.96[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs870225	0.87[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	nsv912817	chr20:23127661-23240969	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1066734	chr20:23170094-23277628	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23214200-23241000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr20:23225600-23235600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:23226400-23234200	Weak transcription	Fetal Kidney	kidney
4	chr20:23226800-23233000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr20:23226800-23237000	Weak transcription	Gastric	stomach
6	chr20:23227000-23232000	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr20:23229200-23236000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr20:23229400-23230800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr20:23230000-23230600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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