Variant report

Variant	rs1521588
Chromosome Location	chr3:146572777-146572778
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10222373	1.00[ASN][1000 genomes]
rs10470459	1.00[ASN][1000 genomes]
rs10470460	1.00[ASN][1000 genomes]
rs10935644	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12330695	1.00[ASN][1000 genomes]
rs12695830	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1319533	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13324524	1.00[ASN][1000 genomes]
rs13324873	1.00[ASN][1000 genomes]
rs13325265	1.00[ASN][1000 genomes]
rs13353410	1.00[ASN][1000 genomes]
rs1402737	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1431967	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1431969	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1521579	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1521580	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2116430	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2116431	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28498057	1.00[ASN][1000 genomes]
rs28539305	1.00[ASN][1000 genomes]
rs2868954	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28729741	1.00[ASN][1000 genomes]
rs56737593	1.00[ASN][1000 genomes]
rs58365455	1.00[ASN][1000 genomes]
rs6783801	1.00[ASN][1000 genomes]
rs6809355	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159171	1.00[ASN][1000 genomes]
rs7610634	1.00[ASN][1000 genomes]
rs7614167	1.00[ASN][1000 genomes]
rs7626080	1.00[ASN][1000 genomes]
rs7636940	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7640043	0.91[CEU][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642381	0.93[EUR][1000 genomes]
rs7642386	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7642952	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650149	1.00[ASN][1000 genomes]
rs9289733	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810942	1.00[ASN][1000 genomes]
rs9814690	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818401	1.00[ASN][1000 genomes]
rs9820879	1.00[ASN][1000 genomes]
rs9826710	1.00[ASN][1000 genomes]
rs9831349	1.00[ASN][1000 genomes]
rs9835696	1.00[ASN][1000 genomes]
rs9836951	1.00[ASN][1000 genomes]
rs9841310	1.00[ASN][1000 genomes]
rs9841704	1.00[ASN][1000 genomes]
rs9847241	1.00[ASN][1000 genomes]
rs9850124	1.00[ASN][1000 genomes]
rs9851720	1.00[ASN][1000 genomes]
rs9852256	1.00[ASN][1000 genomes]
rs9857093	1.00[ASN][1000 genomes]
rs9859125	1.00[ASN][1000 genomes]
rs9860770	1.00[ASN][1000 genomes]
rs9861056	1.00[ASN][1000 genomes]
rs9862802	1.00[ASN][1000 genomes]
rs9863350	1.00[ASN][1000 genomes]
rs9863944	1.00[ASN][1000 genomes]
rs9868411	1.00[ASN][1000 genomes]
rs9868687	1.00[ASN][1000 genomes]
rs9869328	1.00[ASN][1000 genomes]
rs9872644	1.00[ASN][1000 genomes]
rs9874910	1.00[ASN][1000 genomes]
rs9881534	1.00[ASN][1000 genomes]
rs9881735	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv516386	chr3:146366513-146758405	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv591961	chr3:146394094-146725217	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1007875	chr3:146401461-146776618	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv998040	chr3:146416916-146729962	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv536760	chr3:146416916-146729962	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1001931	chr3:146419061-146745361	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1005776	chr3:146511378-146599221	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv965364	chr3:146570227-146584347	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1521588	UBQLN4	cis	parietal	SCAN
rs1521588	HLTF	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146572600-146580400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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