Variant report

Variant	rs6804904
Chromosome Location	chr3:133447231-133447232
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10935085	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1130459	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13066859	0.80[EUR][1000 genomes]
rs35553929	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4078166	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4287912	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4443173	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4854596	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4994581	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6439434	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6439436	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6782434	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8177179	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9824479	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9843635	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9869311	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9872999	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][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	nsv877506	chr3:133423473-133569777	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv933605	chr3:133425907-133680641	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv963279	chr3:133426521-133449029	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv528713	chr3:133437778-133450371	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv829729	chr3:133444871-133620387	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6804904	TF	cis	Esophagus Mucosa	GTEx
rs6804904	TFP1	cis	Esophagus Mucosa	GTEx
rs6804904	SRPRB	Cis_1M	lymphoblastoid	RTeQTL
rs6804904	TF	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133442000-133453200	Weak transcription	Brain Inferior Temporal Lobe	brain

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