Variant report

Variant	rs11175332
Chromosome Location	chr12:40541627-40541628
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10506145	0.82[MKK][hapmap]
rs10878123	0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10878208	0.85[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs11175256	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs11175260	0.87[ASN][1000 genomes]
rs11175371	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11175401	0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11175405	0.90[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11175422	0.84[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs11175458	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11175540	0.89[ASN][1000 genomes]
rs11175558	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11564115	0.95[JPT][hapmap]
rs12581285	0.83[ASN][1000 genomes]
rs1472117	0.95[JPT][hapmap]
rs1491922	0.83[ASN][1000 genomes]
rs1491923	0.83[ASN][1000 genomes]
rs1491924	0.86[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1491925	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1491942	0.89[JPT][hapmap]
rs17443199	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17458613	0.85[ASN][1000 genomes]
rs17461429	0.92[ASN][1000 genomes]
rs17518546	0.83[ASN][1000 genomes]
rs2046931	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2131088	0.95[JPT][hapmap]
rs2201144	0.95[JPT][hapmap]
rs2253736	0.81[ASN][1000 genomes]
rs2638224	0.84[ASN][1000 genomes]
rs2638244	0.91[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2638247	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2638250	0.81[ASN][1000 genomes]
rs2638268	0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2638269	0.89[ASN][1000 genomes]
rs2638270	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2638271	0.85[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2708437	0.95[JPT][hapmap]
rs2708438	0.95[JPT][hapmap]
rs2708463	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2708465	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2708478	0.81[ASN][1000 genomes]
rs2723269	0.95[JPT][hapmap]
rs28365179	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs72644819	0.89[ASN][1000 genomes]
rs7310104	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs949640	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv899030	chr12:40509341-40580440	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv899031	chr12:40520684-40580440	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv3379462	chr12:40539260-40541633	Enhancers Weak transcription	TF binding region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11175332	LRRK2	cis	Muscle Skeletal	GTEx
rs11175332	LRRK2	cis	cerebellum	SCAN
rs11175332	LRRK2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40532800-40543800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:40541000-40541800	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr12:40541400-40546600	Weak transcription	Primary monocytes fromperipheralblood	blood

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