Variant report

Variant	rs1491923
Chromosome Location	chr12:40591117-40591118
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10878123	0.90[JPT][hapmap]
rs10878208	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175256	0.90[JPT][hapmap]
rs11175332	0.91[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11175371	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs11175401	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs11175405	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11175422	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs11175458	0.88[ASN][1000 genomes]
rs11175540	0.85[ASN][1000 genomes]
rs11175558	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11564115	0.90[JPT][hapmap]
rs12581617	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1472117	0.90[JPT][hapmap]
rs1491922	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491924	0.85[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1491925	0.96[ASN][1000 genomes]
rs1491942	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs17443199	0.90[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs17461429	0.83[ASN][1000 genomes]
rs2046931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131088	0.90[JPT][hapmap]
rs2201144	0.90[JPT][hapmap]
rs2253736	0.84[ASN][1000 genomes]
rs2638224	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2638244	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2638247	0.96[ASN][1000 genomes]
rs2638250	0.92[ASN][1000 genomes]
rs2638268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2638269	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2638270	0.91[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2638271	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs2708437	0.90[JPT][hapmap]
rs2708438	0.90[JPT][hapmap]
rs2708463	0.92[ASN][1000 genomes]
rs2708465	0.95[ASN][1000 genomes]
rs2708478	0.92[ASN][1000 genomes]
rs2723269	0.90[JPT][hapmap]
rs28365179	0.85[JPT][hapmap]
rs72644819	0.85[ASN][1000 genomes]
rs7310104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs949640	0.82[CHD][hapmap];0.90[JPT][hapmap]

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	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1491923	LRRK2	cis	cerebellum	SCAN
rs1491923	KIF21A	cis	cerebellum	SCAN
rs1491923	LRRK2	cis	Artery Tibial	GTEx
rs1491923	SLC2A13	cis	parietal	SCAN
rs1491923	LRRK2	cis	parietal	SCAN
rs1491923	RP11-476D10.1	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40586200-40591600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr12:40589600-40592200	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr12:40590200-40592000	Enhancers	Liver	Liver
4	chr12:40590200-40595400	Weak transcription	Primary B cells from cord blood	blood
5	chr12:40590400-40595200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:40590400-40595600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr12:40590400-40596600	Weak transcription	Primary B cells from peripheral blood	blood
8	chr12:40591000-40595600	Weak transcription	Primary neutrophils fromperipheralblood	blood

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