Variant report

Variant	rs672685
Chromosome Location	chr19:39469886-39469887
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10412049	0.87[CEU][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs11083491	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12977030	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12982592	0.81[EUR][1000 genomes]
rs4803134	0.82[ASN][1000 genomes]
rs4803155	0.82[ASN][1000 genomes]
rs7253187	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[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	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs672685	PVR	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39467400-39470000	Enhancers	Fetal Intestine Large	intestine
2	chr19:39467400-39470400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:39467400-39471200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr19:39467600-39470400	Weak transcription	K562	blood
5	chr19:39467600-39471400	Weak transcription	Brain Hippocampus Middle	brain
6	chr19:39467600-39471400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr19:39469400-39470400	Weak transcription	Liver	Liver
8	chr19:39469400-39471400	Weak transcription	H1 Derived Mesenchymal Stem 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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