Variant report

Variant	rs875050
Chromosome Location	chr10:90357105-90357106
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10509547	0.82[CEU][hapmap]
rs10509548	0.82[CEU][hapmap]
rs10509549	0.82[CEU][hapmap]
rs10509550	0.82[CEU][hapmap]
rs10736359	0.93[MEX][hapmap];0.86[AMR][1000 genomes]
rs10736360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs10736361	1.00[ASN][1000 genomes]
rs11816967	0.82[CEU][hapmap]
rs1325899	0.81[CEU][hapmap]
rs1325904	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs1359581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359582	0.82[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes]
rs1409133	0.88[AMR][1000 genomes]
rs1409136	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555839	0.95[CEU][hapmap];0.85[CHD][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs1555842	1.00[ASN][1000 genomes]
rs1573074	0.81[CEU][hapmap]
rs1594602	1.00[CHB][hapmap]
rs1653842	1.00[YRI][hapmap]
rs1653843	1.00[YRI][hapmap]
rs1653845	1.00[YRI][hapmap]
rs17336288	0.86[CEU][hapmap]
rs17426488	0.82[CEU][hapmap]
rs1769683	1.00[YRI][hapmap]
rs1769691	1.00[YRI][hapmap]
rs1769692	1.00[YRI][hapmap]
rs1980813	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2057641	1.00[ASN][1000 genomes]
rs2182304	1.00[ASN][1000 genomes]
rs2477959	0.88[AMR][1000 genomes]
rs2576155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576158	0.86[AMR][1000 genomes]
rs2576162	0.82[CEU][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes]
rs2576163	0.80[CEU][hapmap];0.92[AMR][1000 genomes]
rs2576167	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs2765451	0.83[CEU][hapmap]
rs2765453	0.82[CEU][hapmap]
rs2901950	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs372589	1.00[YRI][hapmap]
rs376036	1.00[YRI][hapmap]
rs385397	1.00[YRI][hapmap]
rs390436	1.00[YRI][hapmap]
rs391683	1.00[YRI][hapmap]
rs407433	1.00[YRI][hapmap]
rs408387	1.00[YRI][hapmap]
rs426110	1.00[YRI][hapmap]
rs434401	1.00[YRI][hapmap]
rs437261	1.00[YRI][hapmap]
rs441719	1.00[YRI][hapmap]
rs442545	1.00[YRI][hapmap]
rs447416	1.00[YRI][hapmap]
rs451949	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs454439	1.00[YRI][hapmap]
rs701824	1.00[ASN][1000 genomes]
rs750508	1.00[ASN][1000 genomes]
rs7900987	1.00[ASN][1000 genomes]
rs7913742	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7917696	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814633	1.00[ASN][1000 genomes]
rs814634	1.00[ASN][1000 genomes]
rs814635	1.00[ASN][1000 genomes]
rs860949	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	nsv1044680	chr10:90316066-90466092	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv540740	chr10:90316066-90466092	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1037657	chr10:90329910-90367890	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv551839	chr10:90334835-90422136	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs875050	LIPA	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90356800-90358600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr10:90357000-90358600	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr10:90357000-90360600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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