Variant report

Variant	rs17009398
Chromosome Location	chr1:221279386-221279387
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10746405	0.82[ASN][1000 genomes]
rs10863578	0.85[ASN][1000 genomes]
rs11118641	0.94[ASN][1000 genomes]
rs11118648	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11118652	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11118653	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11118662	0.86[EUR][1000 genomes]
rs11118663	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11118664	0.86[EUR][1000 genomes]
rs12120171	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12121213	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12122167	0.86[EUR][1000 genomes]
rs12123182	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12124230	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12127195	0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12128432	0.83[EUR][1000 genomes]
rs12140672	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1341619	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1539140	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1596173	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17009346	0.94[ASN][1000 genomes]
rs17009529	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17009536	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1935157	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2039956	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3920857	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4142348	0.86[ASN][1000 genomes]
rs4142351	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4391670	0.82[ASN][1000 genomes]
rs4420085	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4427411	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4625285	0.85[ASN][1000 genomes]
rs4846682	0.82[ASN][1000 genomes]
rs4846684	0.83[ASN][1000 genomes]
rs4846685	0.83[ASN][1000 genomes]
rs55966903	0.94[ASN][1000 genomes]
rs57489853	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58513421	0.94[ASN][1000 genomes]
rs59098418	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61819242	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6670400	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6687526	0.83[ASN][1000 genomes]
rs6687905	0.82[ASN][1000 genomes]
rs6693821	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6698945	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67635817	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs715300	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72742507	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7354867	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7511784	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7512831	0.94[ASN][1000 genomes]
rs7515181	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7517729	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7522861	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7523927	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7526270	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7539794	0.84[EUR][1000 genomes]
rs7542237	0.82[ASN][1000 genomes]
rs7544056	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7554672	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9431057	0.86[EUR][1000 genomes]
rs9431425	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9431431	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]

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	nsv997685	chr1:220993527-221863416	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv535299	chr1:220993527-221863416	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv873199	chr1:221136672-221451217	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17009398	LYPLAL1	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221275600-221280600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr1:221278600-221279400	Enhancers	Primary B cells from peripheral blood	blood
3	chr1:221278800-221279400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr1:221279000-221279400	Enhancers	Monocytes-CD14+_RO01746	blood

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