Variant report

Variant	rs55860351
Chromosome Location	chr3:180046977-180046978
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11917884	0.94[EUR][1000 genomes]
rs16831480	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60544006	0.94[EUR][1000 genomes]
rs60640160	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6443695	0.94[EUR][1000 genomes]
rs6786246	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6792973	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73033596	0.94[EUR][1000 genomes]
rs73043166	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044350	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7612449	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7629793	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9823415	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv878041	chr3:179983857-180097855	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:180039000-180047400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:180044800-180047000	Weak transcription	Ovary	ovary
3	chr3:180046600-180047000	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr3:180046600-180047000	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr3:180046600-180047200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:180046800-180048000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:180046800-180048200	Flanking Active TSS	GM12878-XiMat	blood

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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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