Variant report

Variant	rs402781
Chromosome Location	chr10:90526379-90526380
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs12412357	0.80[ASN][1000 genomes]
rs1339780	0.80[ASN][1000 genomes]
rs1339781	0.80[ASN][1000 genomes]
rs1653840	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs17112748	0.80[ASN][1000 genomes]
rs17112781	0.80[ASN][1000 genomes]
rs17112872	0.80[ASN][1000 genomes]
rs17113067	0.87[ASN][1000 genomes]
rs17113082	0.87[ASN][1000 genomes]
rs17113165	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs303469	0.83[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs303470	0.83[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs303472	0.81[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs303473	0.81[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs303476	0.80[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs303477	0.80[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs303480	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303481	0.99[EUR][1000 genomes]
rs303484	0.99[EUR][1000 genomes]
rs303485	0.99[EUR][1000 genomes]
rs303486	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs303490	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303491	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs303493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs303494	0.99[EUR][1000 genomes]
rs303496	0.99[EUR][1000 genomes]
rs303497	1.00[CEU][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs303498	0.97[EUR][1000 genomes]
rs303501	0.99[EUR][1000 genomes]
rs303530	0.97[EUR][1000 genomes]
rs303533	0.97[EUR][1000 genomes]
rs303534	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs303535	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs303536	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs303538	0.93[CEU][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs303540	0.93[EUR][1000 genomes]
rs370117	0.83[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs372444	0.99[EUR][1000 genomes]
rs377183	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs425028	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs438612	0.83[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs444386	0.81[AFR][1000 genomes]
rs450011	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933485	0.85[ASN][1000 genomes]
rs4934421	0.80[ASN][1000 genomes]
rs4934422	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs57934910	0.87[ASN][1000 genomes]
rs58641899	0.80[ASN][1000 genomes]
rs814629	0.83[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs814631	0.83[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs814636	0.93[CEU][hapmap];0.96[TSI][hapmap];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	nsv1052613	chr10:90500521-90526379	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv825502	chr10:90518994-90528513	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs402781	LIPA	cis	parietal	SCAN
rs402781	MMRN2	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90522600-90526600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr10:90523600-90528000	Weak transcription	Ovary	ovary
3	chr10:90523800-90527200	Weak transcription	Hela-S3	cervix
4	chr10:90523800-90527400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr10:90523800-90527800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr10:90525200-90526600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr10:90525600-90526400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr10:90525600-90526400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr10:90525800-90526600	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr10:90526000-90527200	Enhancers	Liver	Liver

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