Variant report

Variant	rs6091909
Chromosome Location	chr20:53132517-53132518
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:53131931..53132565-chr20:53263125..53264081,2	MCF-7	breast:
2	chr20:53131557..53134721-chr20:53135286..53138375,3	MCF-7	breast:
3	chr20:53094603..53097316-chr20:53132108..53133984,2	MCF-7	breast:
4	chr20:53131035..53133953-chr20:53146900..53149514,3	MCF-7	breast:
5	chr20:53131011..53133856-chr20:53139491..53142546,3	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10485786	0.82[CHB][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16999731	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16999732	0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16999736	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.89[MEX][hapmap];0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16999764	0.85[CHD][hapmap]
rs2426520	1.00[EUR][1000 genomes]
rs2426521	1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2426522	0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2426525	1.00[ASN][1000 genomes]
rs2426526	0.98[ASN][1000 genomes]
rs2426529	1.00[CHB][hapmap];0.98[ASN][1000 genomes]
rs2426530	1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs2426531	1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs2426535	0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2426536	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs56977264	1.00[EUR][1000 genomes]
rs57402636	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs57927391	1.00[EUR][1000 genomes]
rs6014025	1.00[EUR][1000 genomes]
rs6014050	0.81[CHD][hapmap]
rs60215168	1.00[EUR][1000 genomes]
rs6023260	1.00[EUR][1000 genomes]
rs6023271	1.00[EUR][1000 genomes]
rs6023344	0.98[ASN][1000 genomes]
rs6091884	1.00[EUR][1000 genomes]
rs6097991	1.00[EUR][1000 genomes]
rs6097995	1.00[EUR][1000 genomes]
rs6098044	1.00[CHB][hapmap];0.98[ASN][1000 genomes]
rs6098064	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6098074	0.85[CHD][hapmap]
rs61495423	1.00[EUR][1000 genomes]
rs62214388	1.00[EUR][1000 genomes]
rs726770	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7272302	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7274532	1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs73276924	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs793039	1.00[EUR][1000 genomes]
rs8126261	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.98[ASN][1000 genomes]
rs974461	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6091909	BCAR3	trans	lymphoblastoid	seeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53118800-53132600	Weak transcription	NHDF-Ad	bronchial
2	chr20:53119600-53137000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr20:53120800-53148800	Weak transcription	Left Ventricle	heart
4	chr20:53127800-53133000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr20:53128600-53142800	Weak transcription	Psoas Muscle	Psoas
6	chr20:53129600-53149200	Weak transcription	Aorta	Aorta
7	chr20:53130600-53133000	Enhancers	Fetal Brain Female	brain
8	chr20:53130600-53134600	Enhancers	Fetal Brain Male	brain
9	chr20:53131400-53133000	Weak transcription	Fetal Kidney	kidney
10	chr20:53131400-53133600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr20:53131400-53140400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr20:53131400-53140800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr20:53132000-53132600	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr20:53132200-53133000	Weak transcription	Brain Anterior Caudate	brain
15	chr20:53132400-53132600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr20:53132400-53132600	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr20:53132400-53132600	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr20:53132400-53133400	Weak transcription	Brain Germinal Matrix	brain
19	chr20:53132400-53140600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr20:53132400-53142000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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