Variant report

Variant	rs59205301
Chromosome Location	chr3:179742479-179742480
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs13324196	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13325206	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56397887	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57729381	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6443685	0.83[AMR][1000 genomes]
rs6443687	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6443688	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6800148	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73883469	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73883479	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7615924	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs939824	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs939825	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs940522	0.83[AMR][1000 genomes]
rs9809603	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9823631	0.83[AMR][1000 genomes]
rs9870941	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829807	chr3:179527567-179745153	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv829808	chr3:179574614-179754321	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv534210	chr3:179666123-179899347	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1000756	chr3:179672703-179827373	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59205301	USP13	cis	inferior olivary nucleus	BrainEAC

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179726000-179754200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:179741000-179745200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:179741000-179750200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:179741800-179743200	Strong transcription	Dnd41	blood
5	chr3:179742400-179742600	Enhancers	Brain Substantia Nigra	brain
6	chr3:179742400-179742600	Enhancers	Pancreas	Pancrea

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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