Variant report

Variant	rs866514
Chromosome Location	chr10:90467067-90467068
allele	G/T
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	chr10:90466849..90468565-chr10:90471171..90472681,2	MCF-7	breast:

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10509554	1.00[ASN][1000 genomes]
rs1214456	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1237989	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1653842	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[MEX][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1653843	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1653845	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs167333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs170004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1769682	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1769683	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1769690	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1769691	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1769692	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1769697	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1769700	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs182493	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs186226	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231778	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs303453	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303454	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303456	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303457	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303464	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];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	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303506	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303507	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303508	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303516	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303517	0.84[AMR][1000 genomes];0.84[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[CHB][hapmap];1.00[ASN][1000 genomes]
rs365847	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs367605	1.00[ASN][1000 genomes]
rs372589	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs376036	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[MEX][hapmap]
rs376045	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs376261	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs377257	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs378308	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[MEX][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs378425	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs385397	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3858283	1.00[ASN][1000 genomes]
rs387970	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs388265	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390414	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390436	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[MEX][hapmap]
rs391683	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399496	1.00[ASN][1000 genomes]
rs406102	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs407433	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[MEX][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs407922	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs408387	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs410033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41284088	1.00[ASN][1000 genomes]
rs412927	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs415996	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs416957	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420381	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs420653	1.00[CEU][hapmap]
rs424371	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs426110	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs426118	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs426836	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs427687	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs432950	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434401	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[MEX][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs435742	1.00[ASN][1000 genomes]
rs437261	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs441719	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs442545	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs442607	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs447416	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs450130	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs450794	0.87[EUR][1000 genomes]
rs451949	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap]
rs454439	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[MEX][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471419	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs516083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55713122	1.00[ASN][1000 genomes]
rs56390975	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61852496	1.00[ASN][1000 genomes]
rs61852497	1.00[ASN][1000 genomes]
rs814617	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814619	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814630	1.00[ASN][1000 genomes]
rs814642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs845134	1.00[CHB][hapmap];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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs866514	LIPN	cis	Whole Blood	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90463200-90468800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr10:90463400-90467200	Weak transcription	Stomach Mucosa	stomach
3	chr10:90465000-90468000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr10:90465000-90468000	Enhancers	HMEC	breast
5	chr10:90465400-90468000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr10:90465600-90468000	Enhancers	NHEK	skin
7	chr10:90465600-90469000	Enhancers	Hela-S3	cervix
8	chr10:90466000-90468400	Enhancers	Muscle Satellite Cultured Cells	--
9	chr10:90466200-90467600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr10:90466200-90468000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr10:90466600-90467600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
12	chr10:90466600-90468000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr10:90466600-90468000	Enhancers	Fetal Lung	lung
14	chr10:90466600-90468000	Enhancers	HSMM	muscle
15	chr10:90466600-90468000	Enhancers	NHDF-Ad	bronchial
16	chr10:90466600-90468000	Enhancers	Osteobl	bone
17	chr10:90466600-90468200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr10:90466600-90468200	Enhancers	HUVEC	blood vessel
19	chr10:90466800-90468200	Enhancers	NH-A	brain
20	chr10:90467000-90467400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
21	chr10:90467000-90467400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr10:90467000-90467400	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr10:90467000-90467600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
24	chr10:90467000-90468000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
25	chr10:90467000-90468000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr10:90467000-90468000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr10:90467000-90468000	Flanking Active TSS	A549	lung
28	chr10:90467000-90468400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell

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