Variant report

Variant	rs13096172
Chromosome Location	chr3:46612546-46612547
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1049667	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12185926	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001441	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806701	1.00[ASN][1000 genomes]
rs3806702	0.98[ASN][1000 genomes]
rs3806703	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6769392	1.00[ASN][1000 genomes]
rs6783573	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650998	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs939408	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9682509	0.82[AFR][1000 genomes];1.00[ASN][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	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13096172	TDGF1	cis	Adipose Subcutaneous	GTEx
rs13096172	TDGF1	cis	Muscle Skeletal	GTEx
rs13096172	TDGF1	cis	Nerve Tibial	GTEx
rs13096172	TDGF1	cis	Esophagus Muscularis	GTEx
rs13096172	TDGF1	cis	lung	GTEx
rs13096172	TDGF1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46608200-46613200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:46608200-46616400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:46608400-46613000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:46608400-46613200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:46608400-46614200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:46608400-46614400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:46608400-46617200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:46608400-46625400	Weak transcription	Right Atrium	heart

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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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