Variant report

Variant	rs7125262
Chromosome Location	chr11:16692060-16692061
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:16691188..16692933-chr11:16759171..16761829,2	MCF-7	breast:
2	chr11:16691570..16693601-chr11:16731632..16734150,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110696	Chromatin interaction
ENSG00000110693	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10734249	0.92[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10741708	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12786367	0.85[CEU][hapmap];0.93[CHB][hapmap];0.83[GIH][hapmap]
rs12794768	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12799800	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12799969	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12804277	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1501451	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1846936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1967192	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1995343	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2221243	0.85[EUR][1000 genomes]
rs34097789	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34812104	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3802963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3921675	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4396254	0.85[CEU][hapmap]
rs4756860	0.88[EUR][1000 genomes]
rs4756862	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4757428	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4757431	0.81[GIH][hapmap]
rs4757432	0.82[EUR][1000 genomes]
rs6486310	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6486312	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66670205	0.88[EUR][1000 genomes]
rs7110136	0.91[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7117140	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7125008	0.81[EUR][1000 genomes]
rs7128484	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7939889	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7944906	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7945007	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs7950287	0.85[CEU][hapmap];0.86[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	nsv553566	chr11:16329009-16799044	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	esv3396970	chr11:16658425-16715569	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7125262	C11orf58	cis	cerebellum	SCAN
rs7125262	TSG101	cis	cerebellum	SCAN
rs7125262	SLC6A5	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:16691000-16692200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:16691400-16692200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:16691600-16692400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links