Variant report

Variant	rs7628389
Chromosome Location	chr3:160733506-160733507
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	chr3:160732451..160734009-chr3:160957436..160960399,2	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:86)

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

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160732000-160734200	Enhancers	Colon Smooth Muscle	Colon
2	chr3:160732400-160733800	Enhancers	Left Ventricle	heart
3	chr3:160732600-160733600	Enhancers	Stomach Smooth Muscle	stomach
4	chr3:160732600-160733800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:160732800-160745000	Weak transcription	Psoas Muscle	Psoas
6	chr3:160733000-160733600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:160733000-160733800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:160733000-160734200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:160733000-160735200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:160733200-160733600	Enhancers	Fetal Stomach	stomach
11	chr3:160733200-160733800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:160733400-160736600	Weak transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links