Variant report

Variant	rs34715468
Chromosome Location	chr15:43613943-43613944
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10518812	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12908460	0.85[AMR][1000 genomes]
rs12911569	0.85[AMR][1000 genomes]
rs16957680	0.85[AMR][1000 genomes]
rs16957715	0.85[AMR][1000 genomes]
rs17723479	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs17780417	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs17780920	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2230451	0.85[AMR][1000 genomes]
rs34178146	0.84[AFR][1000 genomes]
rs34591748	0.85[AMR][1000 genomes]
rs34657657	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs34661349	0.83[AMR][1000 genomes]
rs34767197	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs34860428	0.85[AMR][1000 genomes]
rs35158584	0.85[AMR][1000 genomes]
rs35160541	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs35278805	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs35311230	0.93[AFR][1000 genomes]
rs35326382	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs35992154	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs55748552	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs62019432	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs62021180	0.85[AMR][1000 genomes]
rs7176923	0.85[AMR][1000 genomes]
rs7177892	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7180812	0.85[AMR][1000 genomes]
rs7181545	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7181634	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7183708	0.83[AMR][1000 genomes]
rs72707530	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv534649	chr15:43591116-43851142	Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs34715468	TGM7	cis	Esophagus Mucosa	GTEx
rs34715468	TUBGCP4	cis	Artery Tibial	GTEx
rs34715468	LCMT2	cis	Esophagus Mucosa	GTEx
rs34715468	ZSCAN29	cis	multi-tissue	Pritchard

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43609000-43620200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr15:43611600-43620200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr15:43613000-43620600	Weak transcription	Right Atrium	heart
4	chr15:43613600-43620200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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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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