Variant report

Variant	rs9883566
Chromosome Location	chr3:160770323-160770324
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	chr3:160768929..160771201-chr3:160940766..160943445,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271052	Chromatin interaction
ENSG00000169251	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10154889	0.85[CEU][hapmap];0.90[AMR][1000 genomes]
rs10433352	0.81[JPT][hapmap];0.81[MEX][hapmap];0.91[AMR][1000 genomes]
rs11711152	0.90[CEU][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.82[TSI][hapmap]
rs11713093	0.84[JPT][hapmap]
rs11715733	0.91[AMR][1000 genomes]
rs11717272	1.00[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11718966	0.90[CEU][hapmap];0.85[JPT][hapmap]
rs11720263	1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11915989	0.85[EUR][1000 genomes]
rs11922957	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11922959	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12696112	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12696113	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13060601	0.89[EUR][1000 genomes]
rs13060718	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13062651	0.87[AMR][1000 genomes]
rs13071892	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13071999	0.90[CEU][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];0.85[TSI][hapmap]
rs13073059	0.90[CEU][hapmap];0.80[JPT][hapmap]
rs13085336	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[EUR][1000 genomes]
rs13098896	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13256	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13315565	0.94[CEU][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1345156	0.90[CEU][hapmap];0.93[GIH][hapmap];0.85[TSI][hapmap]
rs1374787	0.81[JPT][hapmap]
rs1447610	0.90[CEU][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.85[TSI][hapmap]
rs1447622	0.94[CEU][hapmap]
rs1562464	0.90[CEU][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1599388	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16831796	0.82[CHD][hapmap];0.86[MEX][hapmap];0.94[AMR][1000 genomes]
rs16831886	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1868105	0.90[CEU][hapmap]
rs1868107	0.90[CEU][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.82[TSI][hapmap]
rs2014810	0.91[AMR][1000 genomes]
rs2044571	0.90[CEU][hapmap];0.85[JPT][hapmap]
rs2889390	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs34221255	0.82[AMR][1000 genomes]
rs34630898	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35914913	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4494975	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4521287	1.00[CEU][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4679920	0.90[CEU][hapmap];0.84[JPT][hapmap]
rs4679929	0.89[AMR][1000 genomes]
rs4856700	0.90[CEU][hapmap]
rs57145341	0.94[AMR][1000 genomes]
rs6441338	0.94[CEU][hapmap];0.85[JPT][hapmap]
rs6441362	0.89[EUR][1000 genomes]
rs6768115	0.90[CEU][hapmap];0.80[JPT][hapmap];0.82[TSI][hapmap]
rs6772723	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs6774725	0.90[CEU][hapmap]
rs6794882	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6801444	0.90[CEU][hapmap]
rs6806015	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs68166680	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73021215	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73023235	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7433918	0.81[AMR][1000 genomes]
rs7610432	0.91[AMR][1000 genomes]
rs7618455	0.80[AMR][1000 genomes]
rs7618924	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7624185	0.90[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7628389	0.81[CHD][hapmap];0.81[MEX][hapmap];0.90[AMR][1000 genomes]
rs7641892	0.90[CEU][hapmap];0.85[JPT][hapmap]
rs898677	0.81[MEX][hapmap];0.91[AMR][1000 genomes]
rs935497	0.90[CEU][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.85[TSI][hapmap]
rs964533	0.90[CEU][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9812507	0.90[CEU][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9822435	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9832109	0.90[CEU][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9844267	0.89[CEU][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];0.83[TSI][hapmap]
rs9845943	0.90[CEU][hapmap];0.95[GIH][hapmap];0.83[TSI][hapmap]
rs9857482	0.90[CEU][hapmap]
rs9857855	0.81[JPT][hapmap];0.91[AMR][1000 genomes]
rs9860537	0.90[CEU][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap]
rs9862086	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9876142	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9880269	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9883566	B3GALNT1	cis	lymphoblastoid	seeQTL
rs9883566	C3orf57	cis	parietal	SCAN
rs9883566	NMD3	cis	parietal	SCAN
rs9883566	PPM1L	cis	cerebellum	SCAN
rs9883566	SPTSSB	cis	Thyroid	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160745200-160782600	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr3:160768000-160778000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:160768000-160786400	Weak transcription	Left Ventricle	heart
4	chr3:160769000-160770600	Weak transcription	Primary B cells from cord blood	blood
5	chr3:160769200-160772400	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links