Variant report

Variant	rs1319533
Chromosome Location	chr3:146536065-146536066
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:146535974..146536861-chr3:146909343..146910183,2	MCF-7	breast:
2	chr3:146535595..146536102-chr3:147133508..147134222,2	MCF-7	breast:

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10222373	1.00[ASN][1000 genomes]
rs10470459	1.00[ASN][1000 genomes]
rs10470460	1.00[ASN][1000 genomes]
rs10935644	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12330695	1.00[ASN][1000 genomes]
rs12695830	0.95[AMR][1000 genomes];1.00[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	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1431967	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1431969	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1521579	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1521580	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1521588	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17368735	1.00[ASN][1000 genomes]
rs2116430	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2116431	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28498057	1.00[ASN][1000 genomes]
rs28539305	1.00[ASN][1000 genomes]
rs2868954	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28729741	1.00[ASN][1000 genomes]
rs55848109	1.00[ASN][1000 genomes]
rs56737593	1.00[ASN][1000 genomes]
rs58365455	1.00[ASN][1000 genomes]
rs6771456	1.00[ASN][1000 genomes]
rs6783801	1.00[ASN][1000 genomes]
rs6808571	1.00[ASN][1000 genomes]
rs6809355	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159103	1.00[ASN][1000 genomes]
rs73159127	1.00[ASN][1000 genomes]
rs73159146	1.00[ASN][1000 genomes]
rs73159151	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	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7640043	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642381	0.81[EUR][1000 genomes]
rs7642386	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7642952	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650149	1.00[ASN][1000 genomes]
rs9289733	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810942	1.00[ASN][1000 genomes]
rs9814690	1.00[AMR][1000 genomes];0.98[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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv1005776	chr3:146511378-146599221	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv460881	chr3:146512753-146569037	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	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
rs1319533	UBQLN4	cis	parietal	SCAN
rs1319533	HLTF	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146533000-146541600	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:146533200-146536200	Weak transcription	HSMM	muscle
3	chr3:146533600-146536200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:146534600-146536200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:146534600-146539400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:146535400-146537000	Enhancers	Dnd41	blood
7	chr3:146535600-146536400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:146535600-146536800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:146536000-146536800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:146536000-146537000	Enhancers	Muscle Satellite Cultured Cells	--

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