Variant report

Variant	rs2808630
Chromosome Location	chr1:159680868-159680869
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10797052	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10797053	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11265268	0.80[ASN][1000 genomes]
rs12734169	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2808627	0.89[ASN][1000 genomes]
rs2808634	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3116650	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3116652	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3122014	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4255379	0.80[ASN][1000 genomes]
rs4275453	0.80[EUR][1000 genomes]
rs4420078	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs4425982	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4433388	0.80[ASN][1000 genomes]
rs4656848	0.83[ASN][1000 genomes]
rs4656849	0.80[ASN][1000 genomes]
rs6677719	0.80[ASN][1000 genomes]
rs876538	0.87[ASW][hapmap]

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	nsv1005195	chr1:159452759-159910337	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Lung cancer	18385676	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2808630	FDPS	cis	parietal	SCAN
rs2808630	PMVK	cis	parietal	SCAN
rs2808630	DCAF8	cis	parietal	SCAN
rs2808630	B4GALT3	cis	parietal	SCAN
rs2808630	PMF1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159669800-159682000	Weak transcription	Fetal Intestine Large	intestine
2	chr1:159678200-159681600	Weak transcription	Fetal Intestine Small	intestine
3	chr1:159680800-159683400	Active TSS	Liver	Liver

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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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