Variant report

Variant	rs303541
Chromosome Location	chr10:90560417-90560418
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr10:90560214-90561030	PBDE	blood:	n/a	chr10:90560649-90560656 chr10:90560647-90560656 chr10:90560646-90560658 chr10:90560738-90560747 chr10:90560647-90560657
2	GATA3	chr10:90560361-90561049	SK-N-SH	brain:	n/a	chr10:90560649-90560656 chr10:90560647-90560656 chr10:90560646-90560658 chr10:90560738-90560747 chr10:90560647-90560657
3	POLR2A	chr10:90559946-90560422	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
LIPM	TF binding region

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10509554	1.00[ASN][1000 genomes]
rs1237989	1.00[ASN][1000 genomes]
rs1653842	1.00[CHB][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]
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	1.00[CHB][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]
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	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303468	1.00[ASN][1000 genomes]
rs303474	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303478	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303479	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303482	1.00[ASN][1000 genomes]
rs303483	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303488	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303489	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303500	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303502	0.98[AMR][1000 genomes];1.00[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]
rs303531	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303532	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303537	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303539	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs365847	1.00[ASN][1000 genomes]
rs367605	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs372589	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs376036	1.00[CHB][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[ASN][1000 genomes]
rs378425	1.00[ASN][1000 genomes]
rs385397	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3858283	0.96[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	1.00[CHB][hapmap]
rs391683	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs399496	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs406102	1.00[ASN][1000 genomes]
rs407433	1.00[CHB][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[ASN][1000 genomes]
rs435742	0.98[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]
rs442607	1.00[ASN][1000 genomes]
rs447416	1.00[CHB][hapmap]
rs450130	1.00[ASN][1000 genomes]
rs451949	1.00[CHB][hapmap]
rs454439	1.00[CHB][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	0.98[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[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs866514	1.00[ASN][1000 genomes]

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
rs303541	LIPN	cis	Whole Blood	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90555600-90560600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr10:90560200-90561000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr10:90560200-90561000	Enhancers	Muscle Satellite Cultured Cells	--
4	chr10:90560200-90561000	Enhancers	Osteobl	bone
5	chr10:90560400-90560800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr10:90560400-90561000	Enhancers	NH-A	brain
7	chr10:90560400-90561200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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