Variant report

Variant	rs12529948
Chromosome Location	chr6:128859484-128859485
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	chr6:128858016..128860798-chr6:128866625..128868395,2	MCF-7	breast:
2	chr6:128848166..128851056-chr6:128858562..128860170,2	MCF-7	breast:

Extended variants
information (count: 132 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10085245	1.00[ASN][1000 genomes]
rs10085247	1.00[ASN][1000 genomes]
rs10085248	1.00[ASN][1000 genomes]
rs10223535	1.00[ASN][1000 genomes]
rs10872331	1.00[ASN][1000 genomes]
rs11154439	1.00[ASN][1000 genomes]
rs11154440	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751628	1.00[ASN][1000 genomes]
rs11752256	1.00[ASN][1000 genomes]
rs11753496	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11758545	1.00[ASN][1000 genomes]
rs11758690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11963575	1.00[ASN][1000 genomes]
rs12524679	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525214	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12526634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12526667	1.00[ASN][1000 genomes]
rs12527086	0.86[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12527265	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12529229	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12529511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12529947	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1341584	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1341585	0.86[CEU][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1341588	0.83[EUR][1000 genomes]
rs13437323	1.00[ASN][1000 genomes]
rs1417896	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1572964	0.93[CEU][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17055952	1.00[ASN][1000 genomes]
rs17056043	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17364020	1.00[ASN][1000 genomes]
rs17364090	1.00[ASN][1000 genomes]
rs17364118	1.00[ASN][1000 genomes]
rs17364153	1.00[ASN][1000 genomes]
rs17461370	1.00[ASN][1000 genomes]
rs17461759	0.86[CEU][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs1935131	1.00[ASN][1000 genomes]
rs2144376	1.00[CEU][hapmap]
rs2326702	1.00[ASN][1000 genomes]
rs55988836	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57922933	1.00[ASN][1000 genomes]
rs62425737	1.00[ASN][1000 genomes]
rs62425738	1.00[ASN][1000 genomes]
rs62425739	1.00[ASN][1000 genomes]
rs62425740	1.00[ASN][1000 genomes]
rs62425742	1.00[ASN][1000 genomes]
rs62425743	1.00[ASN][1000 genomes]
rs62425744	1.00[ASN][1000 genomes]
rs62426790	1.00[ASN][1000 genomes]
rs62426791	1.00[ASN][1000 genomes]
rs62426792	1.00[ASN][1000 genomes]
rs62426793	1.00[ASN][1000 genomes]
rs62426794	1.00[ASN][1000 genomes]
rs62426795	1.00[ASN][1000 genomes]
rs62426796	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426797	1.00[ASN][1000 genomes]
rs62426798	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426799	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426800	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62426801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426806	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426840	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426841	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426845	0.96[EUR][1000 genomes]
rs62426846	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426847	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426848	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426849	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426850	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426851	1.00[ASN][1000 genomes]
rs62426853	1.00[ASN][1000 genomes]
rs62427780	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62427781	1.00[ASN][1000 genomes]
rs6569529	1.00[ASN][1000 genomes]
rs6569535	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs6569536	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs6916294	0.94[EUR][1000 genomes]
rs714782	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs717617	0.87[CEU][hapmap]
rs7356818	1.00[ASN][1000 genomes]
rs7356823	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs7356912	1.00[ASN][1000 genomes]
rs7454742	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs766306	1.00[ASN][1000 genomes]
rs7738739	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7739600	1.00[ASN][1000 genomes]
rs7748742	1.00[ASN][1000 genomes]
rs7751094	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751265	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs7752487	1.00[ASN][1000 genomes]
rs7754729	0.99[EUR][1000 genomes]
rs7760287	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760572	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760682	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7765212	1.00[ASN][1000 genomes]
rs7768240	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7771701	1.00[ASN][1000 genomes]
rs9321122	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375578	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs9388647	0.99[EUR][1000 genomes]
rs9388648	0.94[EUR][1000 genomes]
rs9388649	0.99[EUR][1000 genomes]
rs9388650	0.99[EUR][1000 genomes]
rs9402055	0.99[EUR][1000 genomes]
rs9482892	1.00[ASN][1000 genomes]
rs9482893	1.00[ASN][1000 genomes]
rs9482897	1.00[ASN][1000 genomes]
rs9482902	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9482904	1.00[ASN][1000 genomes]
rs9491988	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492000	0.86[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492002	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492003	0.99[EUR][1000 genomes]
rs9492004	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492005	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492008	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492011	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492013	1.00[ASN][1000 genomes]
rs9492014	1.00[ASN][1000 genomes]
rs9492017	1.00[CEU][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492018	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492020	1.00[ASN][1000 genomes]
rs9492021	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv830800	chr6:128710631-128878435	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128858800-128860000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr6:128859200-128859600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:128859200-128859800	Enhancers	Primary hematopoietic stem cells	blood
4	chr6:128859400-128862200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:128859400-128863000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links