Variant report

Variant	rs288190
Chromosome Location	chr5:107338352-107338353
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:107332693..107334247-chr5:107337068..107339147,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10477882	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs176385	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs188275	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2116823	0.89[CHD][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap]
rs2416521	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs288180	0.82[TSI][hapmap]
rs288183	0.96[TSI][hapmap]
rs288187	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs288188	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs288191	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs288193	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2916577	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6596762	0.90[CHB][hapmap]
rs6867577	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs6882731	0.86[CHD][hapmap]
rs6886766	0.86[CHD][hapmap]
rs6896080	0.90[CHB][hapmap]
rs7444532	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7707026	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7716454	0.81[CHD][hapmap]
rs7721143	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs8180405	0.91[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs867912	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9328026	0.90[CHB][hapmap]
rs967489	0.90[CHB][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	nsv882682	chr5:107213361-107458336	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv327830	chr5:107337906-107340794	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs288190	FER	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107319800-107354000	Weak transcription	Primary B cells from cord blood	blood
2	chr5:107321200-107338800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr5:107327400-107353400	Weak transcription	Aorta	Aorta
4	chr5:107333800-107338400	Weak transcription	NHDF-Ad	bronchial
5	chr5:107333800-107338800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:107333800-107338800	Weak transcription	Fetal Brain Male	brain
7	chr5:107334200-107338600	Weak transcription	HUVEC	blood vessel
8	chr5:107336800-107338600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr5:107338200-107338400	Enhancers	Dnd41	blood

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