Variant report

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr21:18012604-18012894	HepG2	liver:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-USP25-3	chr21:18012549-18012952	ENSG00000228798
2	lnc-USP25-3	chr21:18012549-18013002	ENSG00000228798
3	lnc-USP25-3	chr21:18012512-18017814	NONHSAT081261
4	lnc-USP25-3	chr21:18012549-18012950	NONHSAT081262

Variant related genes	Relation type
ENSG00000270093	TF binding region

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11088586	0.86[EUR][1000 genomes]
rs1116415	0.93[EUR][1000 genomes]
rs1129247	0.93[EUR][1000 genomes]
rs11702837	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12626359	0.86[EUR][1000 genomes]
rs12626360	0.93[EUR][1000 genomes]
rs12627380	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12627437	0.86[EUR][1000 genomes]
rs12627532	0.93[EUR][1000 genomes]
rs13051672	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13052472	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2027623	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2027624	0.94[EUR][1000 genomes]
rs2027625	0.94[EUR][1000 genomes]
rs2154727	0.93[EUR][1000 genomes]
rs2211987	0.93[EUR][1000 genomes]
rs2211988	0.93[EUR][1000 genomes]
rs2211990	0.93[EUR][1000 genomes]
rs2823929	0.94[EUR][1000 genomes]
rs2823930	0.94[EUR][1000 genomes]
rs2823931	0.93[EUR][1000 genomes]
rs2823932	0.93[EUR][1000 genomes]
rs2823933	0.91[EUR][1000 genomes]
rs4485639	0.93[EUR][1000 genomes]
rs4485640	0.93[EUR][1000 genomes]
rs7279043	0.91[EUR][1000 genomes]
rs7281452	0.81[ASN][1000 genomes]
rs8133801	0.93[EUR][1000 genomes]
rs8134854	0.93[EUR][1000 genomes]
rs9637008	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9980343	0.88[EUR][1000 genomes]
rs9984100	0.93[EUR][1000 genomes]
rs9984105	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064857	chr21:17628760-18533131	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	345 gene(s)	inside rSNPs	diseases
2	nsv544382	chr21:17628760-18533131	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	345 gene(s)	inside rSNPs	diseases
3	nsv834052	chr21:17967385-18142224	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13050616	AP000473.8	cis	Thyroid	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:18003600-18015400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr21:18008000-18019000	Weak transcription	Fetal Brain Male	brain
3	chr21:18012800-18013200	Enhancers	Adipose Nuclei	Adipose
4	chr21:18012800-18013200	Active TSS	Liver	Liver

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