Variant report

Variant	rs9309820
Chromosome Location	chr3:78900576-78900577
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12714473	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1480687	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1480688	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs162870	0.88[CEU][hapmap]
rs1843786	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs439325	0.84[CEU][hapmap]
rs9309819	0.84[CEU][hapmap]
rs9835958	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9837982	0.92[CEU][hapmap]
rs9863758	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs9877603	0.96[CEU][hapmap]
rs9881587	1.00[CEU][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78896600-78904200	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:78896600-78908400	Weak transcription	Osteobl	bone
3	chr3:78897200-78907200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:78897800-78900600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:78898000-78904400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:78898200-78904200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:78898200-78905000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:78898600-78904200	Weak transcription	Fetal Lung	lung
9	chr3:78898600-78906800	Weak transcription	A549	lung
10	chr3:78899200-78906800	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:78900000-78904200	Weak transcription	HepG2	liver
12	chr3:78900200-78900800	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr3:78900400-78900800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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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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