Variant report

Variant	rs1521580
Chromosome Location	chr3:146521978-146521979
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10935644	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12695830	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1319533	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1402737	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1431967	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1431969	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1521579	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1521588	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2116430	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2116431	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2868954	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6809355	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7636940	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7640043	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7642381	0.81[EUR][1000 genomes]
rs7642386	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7642952	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9289733	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9814690	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9881735	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv877624	chr3:146414837-146536741	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	nsv877625	chr3:146461435-146521978	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1005776	chr3:146511378-146599221	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv460881	chr3:146512753-146569037	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv591962	chr3:146512753-146569037	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1521580	HLTF	cis	cerebellum	SCAN
rs1521580	UBQLN4	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146519200-146523000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr3:146519400-146522000	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr3:146519600-146522000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:146519600-146532800	Weak transcription	NHLF	lung
5	chr3:146520000-146523000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:146520400-146522000	Enhancers	Dnd41	blood
7	chr3:146520400-146523000	Enhancers	NHDF-Ad	bronchial
8	chr3:146520600-146522400	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr3:146521000-146522200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:146521000-146522200	Enhancers	Osteobl	bone
11	chr3:146521000-146522600	Enhancers	Muscle Satellite Cultured Cells	--
12	chr3:146521200-146522400	Enhancers	HSMM	muscle
13	chr3:146521200-146522600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:146521400-146522000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr3:146521400-146522000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:146521600-146522000	Enhancers	HUES48 Cell Line	embryonic stem cell

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