Variant report

Variant	rs303500
Chromosome Location	chr10:90553417-90553418
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	chr10:90548383..90549951-chr10:90552065..90554199,2	MCF-7	breast:

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	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303468	1.00[ASN][1000 genomes]
rs303474	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303478	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303479	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303482	1.00[ASN][1000 genomes]
rs303483	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303488	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303489	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303502	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]
rs303531	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303532	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303537	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303539	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs303541	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs365847	1.00[ASN][1000 genomes]
rs367605	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[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	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[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	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[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	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[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	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814642	1.00[ASN][1000 genomes]
rs845134	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[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
rs303500	LIPN	cis	Whole Blood	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90550600-90554000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr10:90551000-90555000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr10:90551400-90554600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr10:90551600-90553600	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr10:90551800-90553600	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr10:90551800-90554800	Enhancers	Muscle Satellite Cultured Cells	--
7	chr10:90551800-90555000	Enhancers	Osteobl	bone
8	chr10:90552000-90554000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr10:90552000-90555600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr10:90552200-90554000	Enhancers	HMEC	breast
11	chr10:90552200-90554000	Enhancers	NH-A	brain
12	chr10:90552200-90554200	Enhancers	GM12878-XiMat	blood
13	chr10:90552200-90554800	Enhancers	NHDF-Ad	bronchial
14	chr10:90552200-90555000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr10:90552400-90554000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr10:90552400-90554800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr10:90552800-90553800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr10:90552800-90553800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr10:90552800-90553800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr10:90552800-90553800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr10:90552800-90554800	Enhancers	Hela-S3	cervix
22	chr10:90553000-90554400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr10:90553200-90553600	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr10:90553200-90554200	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr10:90553200-90560400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr10:90553400-90553600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr10:90553400-90553800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr10:90553400-90554000	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr10:90553400-90554000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr10:90553400-90554200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr10:90553400-90554200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr10:90553400-90554200	Enhancers	NHEK	skin
33	chr10:90553400-90554200	Enhancers	NHLF	lung
34	chr10:90553400-90554400	Enhancers	A549	lung

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