Variant report

Variant	rs10509554
Chromosome Location	chr10:90525792-90525793
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
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	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1653843	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]
rs1769682	1.00[CHB][hapmap]
rs1769683	1.00[CHB][hapmap]
rs1769690	1.00[ASN][1000 genomes]
rs1769691	1.00[ASN][1000 genomes]
rs1769692	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[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	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]
rs303526	1.00[CHD][hapmap]
rs303531	1.00[ASN][1000 genomes]
rs303532	1.00[ASN][1000 genomes]
rs303537	1.00[ASN][1000 genomes]
rs303541	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs365847	1.00[ASN][1000 genomes]
rs367605	1.00[ASN][1000 genomes]
rs372589	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs376036	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[ASN][1000 genomes]
rs387970	1.00[ASN][1000 genomes]
rs388265	1.00[ASN][1000 genomes]
rs390414	1.00[ASN][1000 genomes]
rs390436	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs391683	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs399496	1.00[ASN][1000 genomes]
rs406102	1.00[ASN][1000 genomes]
rs407433	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	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs435742	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	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]
rs61852497	1.00[ASN][1000 genomes]
rs814617	1.00[ASN][1000 genomes]
rs814619	1.00[ASN][1000 genomes]
rs814630	1.00[ASN][1000 genomes]
rs814642	1.00[ASN][1000 genomes]
rs845134	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs866514	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	nsv1052613	chr10:90500521-90526379	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv825502	chr10:90518994-90528513	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10509554	LIPN	cis	Whole Blood	GTEx
rs10509554	LIPN	cis	lung	GTEx
rs10509554	RCBTB2P1	cis	Whole Blood	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90522600-90526600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr10:90523600-90528000	Weak transcription	Ovary	ovary
3	chr10:90523800-90527200	Weak transcription	Hela-S3	cervix
4	chr10:90523800-90527400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr10:90523800-90527800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr10:90525200-90526600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr10:90525600-90525800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr10:90525600-90526000	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr10:90525600-90526200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr10:90525600-90526400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr10:90525600-90526400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links