Variant report

Variant	rs1520616
Chromosome Location	chr3:180100320-180100321
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1497892	0.83[AMR][1000 genomes]
rs1497893	0.83[AMR][1000 genomes]
rs1607767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16831534	0.83[AMR][1000 genomes]
rs16831600	0.83[AMR][1000 genomes]
rs16831605	0.83[AMR][1000 genomes]
rs16831609	0.83[AMR][1000 genomes]
rs16831612	0.83[AMR][1000 genomes]
rs16831616	0.83[AMR][1000 genomes]
rs16831618	0.83[AMR][1000 genomes]
rs2878952	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41324548	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56939966	0.83[AMR][1000 genomes]
rs73033570	0.85[AMR][1000 genomes]
rs73033579	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73035612	0.83[AMR][1000 genomes]
rs73041700	0.83[AMR][1000 genomes]
rs73043179	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73043710	0.83[AMR][1000 genomes]
rs73043715	0.83[AMR][1000 genomes]
rs73043718	0.83[AMR][1000 genomes]
rs73043790	0.83[AMR][1000 genomes]
rs73043794	0.83[AMR][1000 genomes]
rs73043796	0.83[AMR][1000 genomes]
rs73044349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73044398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73044400	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7629836	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9682924	0.83[AMR][1000 genomes]
rs9882220	0.85[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	nsv1012271	chr3:179806875-180234871	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv878040	chr3:179823887-180128288	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv997388	chr3:179899279-180172349	Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv536817	chr3:179899279-180172349	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1520616	USP13	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:180100000-180100800	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr3:180100000-180101800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:180100200-180100400	Enhancers	HSMMtube	muscle
4	chr3:180100200-180101000	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr3:180100200-180101000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:180100200-180102200	Enhancers	HMEC	breast

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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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