Variant report

Variant	rs9872790
Chromosome Location	chr3:143238874-143238875
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12107201	1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs12107992	1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs1405018	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1525864	0.91[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs16853716	1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs1837611	1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs3849196	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58829294	0.91[ASN][1000 genomes]
rs58992171	0.91[ASN][1000 genomes]
rs6769520	0.95[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs7624412	0.95[CHB][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs973826	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9821051	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9828276	1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs9873052	1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs9873297	0.91[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs9883866	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs996017	1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[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	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	esv2757894	chr3:142992697-143285979	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2759184	chr3:142992697-143285979	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv979886	chr3:143230589-143241439	Weak transcription Enhancers Strong transcription Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143212600-143247400	Weak transcription	Primary T cells from cord blood	blood
2	chr3:143223000-143256200	Weak transcription	Esophagus	oesophagus
3	chr3:143227200-143244400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:143228000-143243600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:143228600-143244000	Weak transcription	HSMM	muscle
6	chr3:143233200-143240800	Enhancers	Dnd41	blood
7	chr3:143238400-143239400	Enhancers	Primary B cells from peripheral blood	blood
8	chr3:143238600-143239200	Strong transcription	Primary T regulatory cells fromperipheralblood	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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