Variant report

Variant	rs4054540
Chromosome Location	chr13:37746363-37746364
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11147637	0.82[AMR][1000 genomes]
rs2399397	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56237212	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73177068	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7985933	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9315471	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9594194	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9603141	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9603144	0.96[AMR][1000 genomes];0.92[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4054540	FAM48A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 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	chr13:37743800-37746400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr13:37744200-37747200	Weak transcription	NHLF	lung
4	chr13:37744200-37747600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr13:37744400-37747200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr13:37744600-37746800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr13:37744600-37747200	Weak transcription	Osteobl	bone
8	chr13:37745000-37747000	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr13:37745600-37746400	Enhancers	Fetal Lung	lung
10	chr13:37745600-37746400	Enhancers	NHDF-Ad	bronchial
11	chr13:37746200-37746400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr13:37746200-37746400	Flanking Active TSS	Brain Cingulate Gyrus	brain
13	chr13:37746200-37746600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr13:37746200-37746800	Active TSS	Brain Angular Gyrus	brain
15	chr13:37746200-37746800	Active TSS	Brain Substantia Nigra	brain
16	chr13:37746200-37748200	Enhancers	Fetal Muscle Leg	muscle

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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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