Variant report

Variant	rs303498
Chromosome Location	chr10:90551836-90551837
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:90447341..90448054-chr10:90551740..90552344,2	MCF-7	breast:
2	chr10:90503565..90504217-chr10:90551517..90552295,3	MCF-7	breast:
3	chr10:90487971..90489104-chr10:90551438..90552610,4	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1653840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231784	1.00[JPT][hapmap]
rs303469	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs303470	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs303472	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs303473	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs303476	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs303477	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs303480	0.97[EUR][1000 genomes]
rs303481	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs303484	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs303485	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs303486	0.97[EUR][1000 genomes]
rs303490	0.99[EUR][1000 genomes]
rs303491	0.97[EUR][1000 genomes]
rs303492	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs303493	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs303494	1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs303496	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303497	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303501	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303530	0.99[EUR][1000 genomes]
rs303533	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303534	0.94[EUR][1000 genomes]
rs303535	0.91[EUR][1000 genomes]
rs303536	0.94[EUR][1000 genomes]
rs303538	0.93[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs303540	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs370117	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs372444	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs377183	0.97[EUR][1000 genomes]
rs402781	0.97[EUR][1000 genomes]
rs425028	0.97[EUR][1000 genomes]
rs438612	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs450011	0.97[EUR][1000 genomes]
rs814629	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs814631	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs814636	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs303498	LIPA	cis	parietal	SCAN
rs303498	MMRN2	cis	parietal	SCAN

Chromatin state (count:9 , 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	chr10:90551600-90552000	Enhancers	Monocytes-CD14+_RO01746	blood
5	chr10:90551600-90552800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr10:90551600-90553600	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr10:90551800-90553600	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr10:90551800-90554800	Enhancers	Muscle Satellite Cultured Cells	--
9	chr10:90551800-90555000	Enhancers	Osteobl	bone

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