Variant report

Variant	rs303517
Chromosome Location	chr10:90449051-90449052
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	chr10:90447586..90451415-chr10:90455778..90458537,3	MCF-7	breast:

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10509549	1.00[ASN][1000 genomes]
rs10509550	1.00[ASN][1000 genomes]
rs10509554	1.00[ASN][1000 genomes]
rs1169042	1.00[ASN][1000 genomes]
rs1214456	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1237989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1325901	1.00[ASN][1000 genomes]
rs1653842	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1653843	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs167333	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs170004	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17336288	1.00[ASN][1000 genomes]
rs1769690	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1769691	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1769692	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1769697	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1769700	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs182493	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs186226	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765451	1.00[ASN][1000 genomes]
rs303453	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs303454	1.00[ASN][1000 genomes]
rs303456	1.00[ASN][1000 genomes]
rs303457	1.00[ASN][1000 genomes]
rs303464	1.00[ASN][1000 genomes]
rs303467	1.00[ASN][1000 genomes]
rs303468	1.00[ASN][1000 genomes]
rs303474	1.00[ASN][1000 genomes]
rs303478	1.00[ASN][1000 genomes]
rs303479	1.00[ASN][1000 genomes]
rs303482	1.00[ASN][1000 genomes]
rs303483	1.00[ASN][1000 genomes]
rs303488	1.00[ASN][1000 genomes]
rs303489	1.00[ASN][1000 genomes]
rs303500	1.00[ASN][1000 genomes]
rs303502	1.00[ASN][1000 genomes]
rs303505	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303506	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303507	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303508	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303510	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303531	1.00[ASN][1000 genomes]
rs303532	1.00[ASN][1000 genomes]
rs303537	1.00[ASN][1000 genomes]
rs303541	1.00[ASN][1000 genomes]
rs365847	1.00[ASN][1000 genomes]
rs367605	1.00[ASN][1000 genomes]
rs372589	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs376045	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs377257	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs378308	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs378425	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs385397	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3858283	1.00[ASN][1000 genomes]
rs387970	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs388265	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390414	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs391683	1.00[ASN][1000 genomes]
rs399496	1.00[ASN][1000 genomes]
rs406102	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs407433	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs407922	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs408387	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs410033	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41284088	1.00[ASN][1000 genomes]
rs412927	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs415996	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs416957	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs424371	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs426118	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs426836	0.83[AMR][1000 genomes]
rs427687	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs432950	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs434401	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs435742	1.00[ASN][1000 genomes]
rs437261	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs441719	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs442607	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs450130	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs454439	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs516083	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55713122	1.00[ASN][1000 genomes]
rs56390975	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57260181	1.00[ASN][1000 genomes]
rs61852496	1.00[ASN][1000 genomes]
rs61852497	1.00[ASN][1000 genomes]
rs814617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814630	1.00[ASN][1000 genomes]
rs814642	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs845134	1.00[ASN][1000 genomes]
rs866514	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948664	chr10:90076715-90517150	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv430254	chr10:90265420-90500520	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1044680	chr10:90316066-90466092	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv540740	chr10:90316066-90466092	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv831941	chr10:90410488-90587332	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs303517	LIPN	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90441400-90449400	Weak transcription	NHEK	skin
2	chr10:90445600-90453400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr10:90447800-90449600	Weak transcription	Hela-S3	cervix
4	chr10:90448800-90449400	Enhancers	A549	lung
5	chr10:90449000-90449600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links