Variant report

Variant	rs450794
Chromosome Location	chr10:90488204-90488205
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:90487910..90488745-chr10:90570207..90570902,2	MCF-7	breast:
2	chr10:90487971..90489104-chr10:90551438..90552610,4	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1409136	1.00[YRI][hapmap]
rs1653842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1653843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1653845	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs167333	0.85[EUR][1000 genomes]
rs170004	0.85[EUR][1000 genomes]
rs1769682	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1769683	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1769690	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1769691	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1769692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1769697	0.88[EUR][1000 genomes]
rs1769700	0.88[EUR][1000 genomes]
rs182493	0.87[EUR][1000 genomes]
rs186226	0.87[EUR][1000 genomes]
rs1980813	1.00[YRI][hapmap]
rs2231778	1.00[CHB][hapmap]
rs2576167	1.00[YRI][hapmap]
rs303453	0.87[EUR][1000 genomes]
rs303454	0.84[EUR][1000 genomes]
rs303456	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs303457	0.84[EUR][1000 genomes]
rs303464	0.83[EUR][1000 genomes]
rs303505	0.85[EUR][1000 genomes]
rs303506	0.87[EUR][1000 genomes]
rs303507	0.85[EUR][1000 genomes]
rs303508	0.85[EUR][1000 genomes]
rs303510	0.85[EUR][1000 genomes]
rs303541	1.00[CHB][hapmap]
rs365847	0.87[EUR][1000 genomes]
rs372589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs376036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs376045	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs376261	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs377257	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs378308	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs378425	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs385397	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs387970	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs388265	0.87[EUR][1000 genomes]
rs390414	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs390436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs391683	1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs406102	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs407433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs407922	0.88[EUR][1000 genomes]
rs408387	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs410033	0.87[EUR][1000 genomes]
rs412927	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs415996	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs416957	0.93[EUR][1000 genomes]
rs420381	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs420653	1.00[CEU][hapmap]
rs424371	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs426110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs426118	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs426836	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs427687	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs432950	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs434401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs437261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs441719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs442545	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs442607	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs447416	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs450130	0.88[EUR][1000 genomes]
rs451949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs454439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs471419	0.87[EUR][1000 genomes]
rs516083	0.86[EUR][1000 genomes]
rs56390975	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs814642	0.87[EUR][1000 genomes]
rs845134	1.00[CHB][hapmap]
rs866514	0.87[EUR][1000 genomes]
rs875050	1.00[YRI][hapmap]

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	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	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
5	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
6	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
7	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
8	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
9	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
rs450794	LIPN	cis	Whole Blood	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90486200-90490800	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr10:90486400-90490600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr10:90486600-90490400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr10:90487400-90488400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr10:90488000-90488600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr10:90488000-90488800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr10:90488200-90488400	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr10:90488200-90488400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr10:90488200-90488800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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