Variant report

Variant	rs7274532
Chromosome Location	chr20:53162070-53162071
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:53156431..53159299-chr20:53159745..53162526,2	MCF-7	breast:
2	chr20:53158565..53163438-chr20:53165298..53171299,6	MCF-7	breast:
3	chr17:56707753..56709458-chr20:53160643..53162668,2	MCF-7	breast:
4	chr20:53151691..53153238-chr20:53161258..53162843,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212195	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10485786	0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs16999731	0.89[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs16999732	0.89[JPT][hapmap]
rs16999736	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs16999764	0.82[CEU][hapmap];0.86[CHD][hapmap]
rs16999772	0.84[MEX][hapmap];0.88[TSI][hapmap]
rs2426521	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2426522	0.85[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2426525	0.98[ASN][1000 genomes]
rs2426526	0.96[ASN][1000 genomes]
rs2426529	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2426530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2426531	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2426535	1.00[ASN][1000 genomes]
rs2426536	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.97[LWK][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57402636	1.00[ASN][1000 genomes]
rs6014049	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6014050	1.00[CEU][hapmap];0.82[CHD][hapmap]
rs6014052	0.88[TSI][hapmap]
rs6014055	0.88[TSI][hapmap]
rs6014056	0.87[TSI][hapmap]
rs6014057	0.88[TSI][hapmap]
rs6023344	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6023357	0.88[TSI][hapmap]
rs6091909	1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs6098044	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6098064	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6098074	0.85[CEU][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs726770	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7272302	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73276924	0.98[ASN][1000 genomes]
rs8117905	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8126261	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs974461	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9917433	1.00[CEU][hapmap]

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	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
2	nsv1067497	chr20:53146241-53751820	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7274532	RAE1	cis	cerebellum	SCAN
rs7274532	SALL4	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53161400-53162400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr20:53161600-53162600	Enhancers	NH-A	brain
3	chr20:53161600-53163400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr20:53161600-53165400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr20:53161800-53162200	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr20:53161800-53162400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr20:53161800-53163000	Enhancers	Osteobl	bone
8	chr20:53161800-53164000	Weak transcription	Fetal Brain Female	brain
9	chr20:53162000-53162400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr20:53162000-53163000	Weak transcription	Fetal Brain Male	brain

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