Variant report

Variant	rs1560772
Chromosome Location	chr8:121998962-121998963
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1433396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1433398	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1560770	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1613681	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1631704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1655000	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1655006	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1714640	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1714643	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1714644	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1714645	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1714662	0.85[EUR][1000 genomes]
rs1714670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17196510	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2043374	0.86[EUR][1000 genomes]
rs2570067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs892306	0.89[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	nsv465790	chr8:121853405-122185415	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv612114	chr8:121853405-122185415	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv891424	chr8:121873345-122393258	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv891425	chr8:121875083-122025559	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1844734	chr8:121928250-122283585	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1560772	EXT1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:121989800-122001200	Weak transcription	Osteobl	bone
2	chr8:121990200-122001000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr8:121997600-121999000	Enhancers	Fetal Lung	lung
4	chr8:121997800-121999200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr8:121997800-122003000	Enhancers	Fetal Stomach	stomach
6	chr8:121998000-122001600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr8:121998200-121999200	Weak transcription	NHLF	lung
8	chr8:121998200-121999400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr8:121998200-121999800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr8:121998200-122001000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr8:121998200-122001600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr8:121998200-122001600	Weak transcription	HSMM	muscle

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links