Variant report

Variant	rs303499
Chromosome Location	chr10:90553051-90553052
allele	C/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: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10887854	0.84[ASN][1000 genomes]
rs10887855	0.84[ASN][1000 genomes]
rs11202848	0.84[ASN][1000 genomes]
rs11202850	0.84[ASN][1000 genomes]
rs11202851	0.83[ASN][1000 genomes]
rs11202852	0.84[ASN][1000 genomes]
rs11202853	0.85[ASN][1000 genomes]
rs11202855	0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs11202856	0.85[YRI][hapmap]
rs12572022	0.85[ASN][1000 genomes]
rs17112679	0.84[ASN][1000 genomes]
rs17112704	0.84[ASN][1000 genomes]
rs215495	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];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
rs303499	LIPN	cis	Whole Blood	GTEx

Chromatin state (count:27 , 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	chr10:90552000-90553200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr10:90552000-90554000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr10:90552000-90555600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr10:90552200-90554000	Enhancers	HMEC	breast
12	chr10:90552200-90554000	Enhancers	NH-A	brain
13	chr10:90552200-90554200	Enhancers	GM12878-XiMat	blood
14	chr10:90552200-90554800	Enhancers	NHDF-Ad	bronchial
15	chr10:90552200-90555000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr10:90552400-90554000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr10:90552400-90554800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr10:90552600-90553400	Weak transcription	NHLF	lung
19	chr10:90552800-90553400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr10:90552800-90553800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr10:90552800-90553800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr10:90552800-90553800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr10:90552800-90553800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr10:90552800-90554800	Enhancers	Hela-S3	cervix
25	chr10:90553000-90553400	Weak transcription	A549	lung
26	chr10:90553000-90553400	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr10:90553000-90554400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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