Variant report

Variant	rs55921200
Chromosome Location	chr3:49189316-49189317
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11552724	0.85[AMR][1000 genomes]
rs11706189	0.83[EUR][1000 genomes]
rs11710247	0.83[EUR][1000 genomes]
rs11713297	0.83[EUR][1000 genomes]
rs11716614	0.88[AMR][1000 genomes]
rs11718982	0.81[EUR][1000 genomes]
rs11719220	0.83[EUR][1000 genomes]
rs11720460	0.81[EUR][1000 genomes]
rs12715434	0.81[EUR][1000 genomes]
rs13068038	0.81[EUR][1000 genomes]
rs13096406	0.83[EUR][1000 genomes]
rs34566463	0.83[EUR][1000 genomes]
rs34784192	0.81[EUR][1000 genomes]
rs35060561	0.83[EUR][1000 genomes]
rs35185152	0.81[EUR][1000 genomes]
rs35673421	0.85[AMR][1000 genomes]
rs5030795	0.85[AMR][1000 genomes]
rs56004653	0.88[AMR][1000 genomes]
rs56306491	0.89[AMR][1000 genomes]
rs66991555	0.83[EUR][1000 genomes]
rs67286839	0.81[EUR][1000 genomes]
rs71324939	0.81[EUR][1000 genomes]
rs73082362	0.88[AMR][1000 genomes]
rs73084135	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9814987	0.84[EUR][1000 genomes]
rs9826525	0.81[EUR][1000 genomes]
rs9828310	0.81[EUR][1000 genomes]
rs9837237	0.83[EUR][1000 genomes]
rs9837625	0.83[EUR][1000 genomes]
rs9847839	0.81[EUR][1000 genomes]
rs9850917	0.81[EUR][1000 genomes]
rs9855123	0.83[EUR][1000 genomes]
rs9862483	0.83[EUR][1000 genomes]
rs9880088	0.81[EUR][1000 genomes]
rs9990153	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs55921200	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs55921200	WDR6	cis	Esophagus Mucosa	GTEx
rs55921200	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs55921200	WDR6	cis	Adipose Subcutaneous	GTEx
rs55921200	WDR6	cis	Whole Blood	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49172200-49200400	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:49186000-49190800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:49186000-49191200	Weak transcription	Gastric	stomach
4	chr3:49186200-49198800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:49186800-49198800	Weak transcription	Pancreas	Pancrea
6	chr3:49187800-49191200	Weak transcription	Esophagus	oesophagus
7	chr3:49189200-49189400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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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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