Variant report

Variant	rs769990
Chromosome Location	chr1:56067233-56067234
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]
rs1006806	0.95[AFR][1000 genomes]
rs1081177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1165464	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1165470	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12139482	1.00[CHD][hapmap]
rs1304159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1695953	0.95[AFR][1000 genomes]
rs2671244	1.00[YRI][hapmap]
rs769969	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs769972	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs769980	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs769985	1.00[AMR][1000 genomes]
rs769987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs769988	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs769993	0.87[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs769994	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs809491	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs984446	0.85[AFR][1000 genomes];1.00[AMR][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	nsv10184	chr1:55728755-56084833	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv461617	chr1:56055190-56123510	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv546303	chr1:56055190-56123510	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv1014866	chr1:56059054-56129092	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56059600-56076000	Weak transcription	Aorta	Aorta
2	chr1:56063200-56089000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:56065600-56067400	Enhancers	Ovary	ovary
4	chr1:56066600-56067400	Enhancers	Fetal Intestine Large	intestine
5	chr1:56066800-56067800	Weak transcription	Fetal Kidney	kidney
6	chr1:56066800-56068400	Weak transcription	NHDF-Ad	bronchial
7	chr1:56067000-56067400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr1:56067000-56069800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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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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