Variant report

Variant	rs16831609
Chromosome Location	chr3:180174805-180174806
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1497892	1.00[AMR][1000 genomes]
rs1497893	1.00[AMR][1000 genomes]
rs1520616	0.83[AMR][1000 genomes]
rs1607767	0.83[AMR][1000 genomes]
rs16831534	1.00[AMR][1000 genomes]
rs16831600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16831605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16831612	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16831616	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16831618	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2878952	0.83[AMR][1000 genomes]
rs41324548	0.83[AMR][1000 genomes]
rs56939966	1.00[AMR][1000 genomes]
rs57744331	0.89[AFR][1000 genomes]
rs59951082	0.89[AFR][1000 genomes]
rs6767567	0.89[AFR][1000 genomes]
rs6793428	0.91[AFR][1000 genomes]
rs6802873	0.89[AFR][1000 genomes]
rs6803379	0.89[AFR][1000 genomes]
rs73033579	0.83[AMR][1000 genomes]
rs73035612	1.00[AMR][1000 genomes]
rs73041700	1.00[AMR][1000 genomes]
rs73043179	0.83[AMR][1000 genomes]
rs73043710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73043715	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73043718	1.00[AMR][1000 genomes]
rs73043790	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73043794	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73043796	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73044349	0.83[AMR][1000 genomes]
rs73044398	0.83[AMR][1000 genomes]
rs73045707	0.87[AFR][1000 genomes]
rs73045724	0.91[AFR][1000 genomes]
rs7629836	0.83[AMR][1000 genomes]
rs7643519	0.89[AFR][1000 genomes]
rs9682924	1.00[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	nsv1007831	chr3:180162003-180348203	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv536818	chr3:180162003-180348203	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv516634	chr3:180171589-180184614	Weak transcription Enhancers Strong transcription Genic enhancers	lncRNA	n/a	inside rSNPs	n/a

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:180172000-180175000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:180174800-180176000	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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