Variant report

Variant	rs1449004
Chromosome Location	chr3:159081357-159081358
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11921372	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13434321	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1375409	0.87[CEU][hapmap]
rs1448999	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1449000	0.99[ASN][1000 genomes]
rs1449013	0.87[CEU][hapmap]
rs1489922	0.86[CEU][hapmap];0.93[GIH][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1515627	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967363	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2220521	0.86[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs2621302	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4086062	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4679856	0.95[CEU][hapmap];0.82[MEX][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6782775	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7621541	0.95[CEU][hapmap]
rs7643870	0.91[CEU][hapmap];0.80[MEX][hapmap]
rs895877	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9290040	0.95[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap]
rs9880297	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv470971	chr3:158590928-159158217	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv998949	chr3:158774806-159394550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1449004	SCARNA7	cis	cerebellum	SCAN
rs1449004	PTX3	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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