Variant report

Variant	rs1520780
Chromosome Location	chr12:119039725-119039726
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10850995	0.82[ASN][1000 genomes]
rs10850997	0.97[ASN][1000 genomes]
rs11069005	0.80[ASN][1000 genomes]
rs11610340	0.84[CEU][hapmap]
rs11610823	0.81[EUR][1000 genomes]
rs11613463	0.84[EUR][1000 genomes]
rs12304093	0.88[ASN][1000 genomes]
rs1356949	0.83[ASN][1000 genomes]
rs1851093	0.84[CEU][hapmap]
rs2005052	0.92[ASN][1000 genomes]
rs2176906	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2393419	0.80[ASN][1000 genomes]
rs2682738	0.80[EUR][1000 genomes]
rs2730550	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2730551	0.80[EUR][1000 genomes]
rs2730553	0.80[EUR][1000 genomes]
rs2730576	0.84[ASN][1000 genomes]
rs4594061	0.92[ASN][1000 genomes]
rs7302191	0.96[ASN][1000 genomes]
rs767957	0.96[ASN][1000 genomes]
rs7978580	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs956866	0.84[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	nsv930978	chr12:118866332-119450600	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1043906	chr12:118991884-119087146	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1520780	PLBD2	cis	cerebellum	SCAN
rs1520780	RNFT2	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:119038400-119041200	Weak transcription	Pancreas	Pancrea
2	chr12:119038600-119040800	Weak transcription	HepG2	liver
3	chr12:119039600-119040200	Enhancers	hESC Derived CD184+ Endoderm 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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