Variant report

Variant	rs769989
Chromosome Location	chr1:56066503-56066504
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1039294	0.84[CEU][hapmap]
rs10493193	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs10493194	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs10493195	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11206626	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11206627	0.98[EUR][1000 genomes]
rs11206635	0.92[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11206649	0.84[CEU][hapmap]
rs11801001	0.92[CEU][hapmap]
rs11805740	0.92[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12116670	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12117758	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12125730	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12139482	1.00[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap]
rs17418048	0.84[CEU][hapmap]
rs17418151	0.84[CEU][hapmap]
rs17452287	0.84[CEU][hapmap]
rs1846562	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1846563	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61566671	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6588567	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs6670673	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs6680818	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs6681925	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6694680	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6694786	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7519540	0.84[CEU][hapmap]
rs7548272	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs7549716	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7550575	0.84[CEU][hapmap]
rs769970	0.84[AMR][1000 genomes];0.98[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	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	nsv523489	chr1:56038407-56066503	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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:10 , 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	chr1:56065600-56066800	Enhancers	NHDF-Ad	bronchial
4	chr1:56065600-56067000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:56065600-56067000	Enhancers	Fetal Muscle Leg	muscle
6	chr1:56065600-56067400	Enhancers	Ovary	ovary
7	chr1:56066000-56067200	Enhancers	Fetal Lung	lung
8	chr1:56066200-56066600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:56066200-56066800	Enhancers	Fetal Stomach	stomach
10	chr1:56066400-56066800	Enhancers	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links