Variant report

Variant	rs9290069
Chromosome Location	chr3:160890946-160890947
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160889756..160892143-chr3:160937651..160939483,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169251	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1026572	0.92[CEU][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10936223	0.96[EUR][1000 genomes]
rs10936224	0.88[EUR][1000 genomes]
rs12493960	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12631850	0.97[EUR][1000 genomes]
rs13066683	0.82[EUR][1000 genomes]
rs1478568	0.82[AMR][1000 genomes]
rs1599374	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1599376	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1599378	0.89[EUR][1000 genomes]
rs1599379	0.87[EUR][1000 genomes]
rs1599381	0.91[EUR][1000 genomes]
rs1599383	0.82[EUR][1000 genomes]
rs1599386	0.82[EUR][1000 genomes]
rs1599389	0.91[EUR][1000 genomes]
rs1599390	0.91[EUR][1000 genomes]
rs1609688	0.88[EUR][1000 genomes]
rs1610158	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs2306061	0.80[CEU][hapmap]
rs4342141	0.81[CEU][hapmap];0.83[CHB][hapmap];0.81[EUR][1000 genomes]
rs4414866	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs4470535	0.88[AMR][1000 genomes]
rs4557202	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs4616689	0.81[EUR][1000 genomes]
rs4618258	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs4856738	0.85[AMR][1000 genomes]
rs4856768	0.82[AMR][1000 genomes]
rs6441354	0.91[CEU][hapmap];0.83[CHB][hapmap];0.91[EUR][1000 genomes]
rs6765270	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6774635	0.82[EUR][1000 genomes]
rs6778254	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6783085	0.91[EUR][1000 genomes]
rs6789244	0.91[EUR][1000 genomes]
rs6799130	0.90[EUR][1000 genomes]
rs7613358	0.86[AMR][1000 genomes]
rs7614375	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7617204	0.91[EUR][1000 genomes]
rs7619011	0.82[EUR][1000 genomes]
rs7625363	0.89[EUR][1000 genomes]
rs7630768	0.91[EUR][1000 genomes]
rs7633857	0.91[EUR][1000 genomes]
rs7637086	0.91[EUR][1000 genomes]
rs7647285	0.89[EUR][1000 genomes]
rs7650703	0.82[EUR][1000 genomes]
rs7651087	0.91[EUR][1000 genomes]
rs9290065	0.83[CEU][hapmap]
rs9820825	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs9839527	0.82[AMR][1000 genomes]
rs9848239	0.82[EUR][1000 genomes]
rs9867582	0.87[EUR][1000 genomes]
rs9879687	0.86[EUR][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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9290069	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160890200-160892400	Weak transcription	Left Ventricle	heart
2	chr3:160890200-160893000	Weak transcription	HUVEC	blood vessel

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