Variant report

Variant	rs6516749
Chromosome Location	chr21:28357999-28358000
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs13046440	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13048512	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995097	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2830552	1.00[ASN][1000 genomes]
rs2830593	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2830603	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2830616	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2830622	0.87[EUR][1000 genomes]
rs34176988	1.00[ASN][1000 genomes]
rs34663667	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34855936	0.83[ASN][1000 genomes]
rs34956452	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35188003	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35424917	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55933916	1.00[ASN][1000 genomes]
rs56356255	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62216011	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7281442	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8130155	1.00[ASN][1000 genomes]
rs9977754	0.83[ASN][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	nsv1066573	chr21:28096356-28374354	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1057400	chr21:28104936-28359948	Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv834068	chr21:28179670-28360808	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1067475	chr21:28238746-29046707	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6516749	NCRNA00189	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:28346200-28359400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr21:28351800-28416600	Weak transcription	Ovary	ovary

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