Variant report

Variant	rs10433352
Chromosome Location	chr3:160747168-160747169
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160746924..160750622-chr3:160787755..160791172,3	MCF-7	breast:
2	chr3:160746769..160748964-chr3:160821024..160822898,2	MCF-7	breast:
3	chr3:160745725..160748261-chr3:160752866..160755134,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169251	Chromatin interaction
ENSG00000169255	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10154889	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10513560	0.81[CHD][hapmap]
rs11711152	0.81[CEU][hapmap]
rs11712713	0.84[EUR][1000 genomes]
rs11713987	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11715733	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11717272	0.81[MEX][hapmap];0.85[AMR][1000 genomes]
rs11718966	0.81[CEU][hapmap]
rs11720263	0.86[MEX][hapmap];0.84[AMR][1000 genomes]
rs11922957	0.86[AMR][1000 genomes]
rs11922959	0.86[AMR][1000 genomes]
rs12696112	0.86[AMR][1000 genomes]
rs12696113	0.86[AMR][1000 genomes]
rs12696114	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13060718	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13062651	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13071892	0.86[AMR][1000 genomes]
rs13071999	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs13073059	0.81[CEU][hapmap]
rs13098896	0.92[AMR][1000 genomes]
rs13256	0.86[MEX][hapmap];0.86[AMR][1000 genomes]
rs13315565	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1345156	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs1374787	0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1374790	0.84[JPT][hapmap]
rs1374795	0.85[JPT][hapmap]
rs1447610	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs1447622	0.80[CEU][hapmap];0.84[JPT][hapmap]
rs1530636	0.81[CHD][hapmap]
rs1562464	0.81[CEU][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes]
rs1599388	0.84[AMR][1000 genomes]
rs16831796	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16831886	0.85[AMR][1000 genomes]
rs1868105	0.81[CEU][hapmap]
rs1868107	0.81[CEU][hapmap]
rs1868109	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs2014810	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2044571	0.81[CEU][hapmap]
rs2376476	0.84[ASN][1000 genomes]
rs2376477	0.82[ASN][1000 genomes]
rs2889390	0.86[JPT][hapmap]
rs34221255	0.84[EUR][1000 genomes]
rs34630898	0.86[AMR][1000 genomes]
rs35914913	0.87[AMR][1000 genomes]
rs4494975	0.84[AMR][1000 genomes]
rs4521287	0.86[MEX][hapmap];0.87[AMR][1000 genomes]
rs4679920	0.81[CEU][hapmap]
rs4679928	0.82[ASN][1000 genomes]
rs4679929	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57145341	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441338	0.85[CEU][hapmap]
rs6441345	0.83[CHD][hapmap]
rs6441349	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6768115	0.81[CEU][hapmap]
rs6772723	0.81[MEX][hapmap]
rs6774203	0.83[CHD][hapmap]
rs6774725	0.81[CEU][hapmap]
rs6794882	0.83[AMR][1000 genomes]
rs6801444	0.81[CEU][hapmap]
rs6806015	0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs68166680	0.86[AMR][1000 genomes]
rs73021215	0.91[AMR][1000 genomes]
rs73023235	0.84[AMR][1000 genomes]
rs7433918	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7610432	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7611005	0.81[ASN][1000 genomes]
rs7618455	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7618924	0.84[AMR][1000 genomes]
rs7624185	0.81[CEU][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7628389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7641892	0.81[CEU][hapmap]
rs898677	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs935497	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs956447	0.90[JPT][hapmap]
rs964533	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9812507	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9822435	0.81[CEU][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9832109	0.85[ASW][hapmap];0.81[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9844267	0.80[CEU][hapmap]
rs9845943	0.81[CEU][hapmap]
rs9857482	0.81[CEU][hapmap]
rs9857855	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9858335	0.83[CHD][hapmap]
rs9860537	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs9862086	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9876142	0.81[MEX][hapmap];0.90[AMR][1000 genomes]
rs9880269	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9883566	0.81[JPT][hapmap];0.81[MEX][hapmap];0.91[AMR][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
rs10433352	NMD3	cis	parietal	SCAN
rs10433352	PPM1L	cis	cerebellum	SCAN
rs10433352	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL
rs10433352	TRIM59	cis	parietal	SCAN
rs10433352	C3orf57	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160745200-160748800	Weak transcription	Placenta	Placenta
2	chr3:160745200-160782600	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:160745600-160747600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:160746400-160747800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:160746600-160749000	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links