Variant report

Variant	rs10878208
Chromosome Location	chr12:40588408-40588409
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10878123	0.83[JPT][hapmap]
rs11175332	0.85[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs11175371	0.81[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs11175401	0.83[ASN][1000 genomes]
rs11175405	0.90[CHB][hapmap];0.96[ASN][1000 genomes]
rs11175422	0.84[ASN][1000 genomes]
rs11175458	0.88[ASN][1000 genomes]
rs11175540	0.85[ASN][1000 genomes]
rs11175558	0.81[CHB][hapmap]
rs11564115	0.83[JPT][hapmap]
rs12581617	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1491922	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491923	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491924	0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs1491925	0.96[ASN][1000 genomes]
rs1491942	0.83[ASN][1000 genomes]
rs17443199	0.81[CHB][hapmap];0.89[ASN][1000 genomes]
rs17461429	0.83[ASN][1000 genomes]
rs2046931	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2201144	0.83[JPT][hapmap]
rs2253736	0.84[ASN][1000 genomes]
rs2638224	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2638244	0.95[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2638247	0.96[ASN][1000 genomes]
rs2638250	0.92[ASN][1000 genomes]
rs2638268	0.95[CHB][hapmap];0.92[ASN][1000 genomes]
rs2638269	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2638270	0.85[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs2638271	0.95[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs2708437	0.83[JPT][hapmap]
rs2708438	0.83[JPT][hapmap]
rs2708463	0.92[ASN][1000 genomes]
rs2708465	0.95[ASN][1000 genomes]
rs2708478	0.92[ASN][1000 genomes]
rs72644819	0.85[ASN][1000 genomes]
rs7310104	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs949640	0.83[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	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	nsv1045516	chr12:40543200-40589557	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
3	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10878208	RP11-476D10.1	cis	Whole Blood	GTEx
rs10878208	LRRK2	cis	Artery Tibial	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40586000-40591000	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr12:40586200-40591600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr12:40586800-40588800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr12:40587200-40589400	Weak transcription	HUVEC	blood vessel
5	chr12:40587200-40590400	Enhancers	Primary B cells from peripheral blood	blood
6	chr12:40588000-40590400	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr12:40588200-40588600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr12:40588200-40589400	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr12:40588200-40589400	Weak transcription	Primary B cells from cord blood	blood
10	chr12:40588200-40589400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:40588400-40589600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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