Variant report

Variant	rs303502
Chromosome Location	chr10:90554113-90554114
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	chr10:90464724..90467365-chr10:90553765..90555681,2	MCF-7	breast:
2	chr10:90548383..90549951-chr10:90552065..90554199,2	MCF-7	breast:

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10509554	1.00[ASN][1000 genomes]
rs11202898	1.00[CHD][hapmap]
rs11202902	1.00[CHD][hapmap]
rs12254856	1.00[CHD][hapmap]
rs1237989	1.00[ASN][1000 genomes]
rs1411780	1.00[CHD][hapmap]
rs1653842	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1653843	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1653845	1.00[CHB][hapmap]
rs167333	1.00[ASN][1000 genomes]
rs170004	1.00[ASN][1000 genomes]
rs17438148	1.00[MKK][hapmap]
rs17446483	1.00[MKK][hapmap]
rs17447091	1.00[CHB][hapmap]
rs1769682	1.00[CHB][hapmap]
rs1769683	1.00[CHB][hapmap]
rs1769690	1.00[ASN][1000 genomes]
rs1769691	1.00[ASN][1000 genomes]
rs1769692	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1769697	1.00[ASN][1000 genomes]
rs1769700	1.00[ASN][1000 genomes]
rs182493	1.00[ASN][1000 genomes]
rs186226	1.00[ASN][1000 genomes]
rs2231778	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2439707	1.00[CHD][hapmap]
rs303453	1.00[ASN][1000 genomes]
rs303454	1.00[ASN][1000 genomes]
rs303456	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs303457	1.00[ASN][1000 genomes]
rs303464	1.00[ASN][1000 genomes]
rs303467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303468	1.00[ASN][1000 genomes]
rs303474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303482	1.00[ASN][1000 genomes]
rs303483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303488	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303489	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303500	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303505	1.00[ASN][1000 genomes]
rs303506	1.00[ASN][1000 genomes]
rs303507	1.00[ASN][1000 genomes]
rs303508	1.00[ASN][1000 genomes]
rs303510	1.00[ASN][1000 genomes]
rs303516	1.00[ASN][1000 genomes]
rs303517	1.00[ASN][1000 genomes]
rs303525	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs303526	1.00[CHD][hapmap]
rs303531	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303532	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303537	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303539	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs303541	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs365847	1.00[ASN][1000 genomes]
rs367605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs372589	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3758483	1.00[CHD][hapmap]
rs376036	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs376045	1.00[ASN][1000 genomes]
rs376261	1.00[CHB][hapmap]
rs377257	1.00[ASN][1000 genomes]
rs378308	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs378425	1.00[ASN][1000 genomes]
rs385397	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3858283	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs387970	1.00[ASN][1000 genomes]
rs388265	1.00[ASN][1000 genomes]
rs390414	1.00[ASN][1000 genomes]
rs390436	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs391683	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs399496	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs406102	1.00[ASN][1000 genomes]
rs407433	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs407922	1.00[ASN][1000 genomes]
rs408387	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs410033	1.00[ASN][1000 genomes]
rs41284088	1.00[ASN][1000 genomes]
rs412927	1.00[ASN][1000 genomes]
rs415996	1.00[ASN][1000 genomes]
rs416957	1.00[ASN][1000 genomes]
rs420381	1.00[CHB][hapmap]
rs424371	1.00[ASN][1000 genomes]
rs426110	1.00[CHB][hapmap]
rs426118	1.00[ASN][1000 genomes]
rs427687	1.00[ASN][1000 genomes]
rs432950	1.00[ASN][1000 genomes]
rs434401	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs435742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs437261	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs441719	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs442545	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs442607	1.00[ASN][1000 genomes]
rs447416	1.00[CHB][hapmap]
rs450130	1.00[ASN][1000 genomes]
rs451949	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs454439	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs516083	1.00[ASN][1000 genomes]
rs56390975	1.00[ASN][1000 genomes]
rs814617	1.00[ASN][1000 genomes]
rs814619	1.00[ASN][1000 genomes]
rs814630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814642	1.00[ASN][1000 genomes]
rs845134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs866514	1.00[ASN][1000 genomes]
rs983751	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv1043015	chr10:90467067-90593692	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	nsv467415	chr10:90478483-90600865	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	nsv551840	chr10:90478483-90600865	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs303502	LIPN	cis	Whole Blood	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90551000-90555000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr10:90551400-90554600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr10:90551800-90554800	Enhancers	Muscle Satellite Cultured Cells	--
4	chr10:90551800-90555000	Enhancers	Osteobl	bone
5	chr10:90552000-90555600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr10:90552200-90554200	Enhancers	GM12878-XiMat	blood
7	chr10:90552200-90554800	Enhancers	NHDF-Ad	bronchial
8	chr10:90552200-90555000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr10:90552400-90554800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr10:90552800-90554800	Enhancers	Hela-S3	cervix
11	chr10:90553000-90554400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr10:90553200-90554200	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr10:90553200-90560400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr10:90553400-90554200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr10:90553400-90554200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr10:90553400-90554200	Enhancers	NHEK	skin
17	chr10:90553400-90554200	Enhancers	NHLF	lung
18	chr10:90553400-90554400	Enhancers	A549	lung
19	chr10:90553600-90554200	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr10:90553800-90554200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr10:90553800-90554200	Enhancers	Primary T cells fromperipheralblood	blood
22	chr10:90553800-90554200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr10:90553800-90554200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr10:90554000-90554800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links