Variant report

Variant	rs2399397
Chromosome Location	chr13:37743666-37743667
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11147637	0.82[AMR][1000 genomes]
rs4054540	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56237212	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6563513	0.81[EUR][1000 genomes]
rs73177068	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7985933	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8001995	0.81[EUR][1000 genomes]
rs9315471	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9532007	0.81[EUR][1000 genomes]
rs9594194	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9603141	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9603144	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2399397	FAM48A	cis	cerebellum	SCAN
rs2399397	SPG20	cis	cerebellum	SCAN
rs2399397	FRY	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:37739800-37747400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr13:37741400-37745000	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr13:37743000-37744600	Enhancers	NHDF-Ad	bronchial
4	chr13:37743200-37743800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr13:37743200-37744600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr13:37743400-37743800	Enhancers	Fetal Lung	lung
7	chr13:37743400-37744200	Enhancers	NHLF	lung
8	chr13:37743400-37744400	Enhancers	Muscle Satellite Cultured Cells	--
9	chr13:37743400-37744600	Enhancers	Osteobl	bone

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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

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