Variant report

Variant	rs4411336
Chromosome Location	chr12:40069333-40069334
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 120 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10047563	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10219652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10444570	0.94[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10735885	1.00[CEU][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10747825	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10747853	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10747877	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10747878	1.00[CEU][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10783959	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs10783969	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs10783993	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10783994	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783998	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10784001	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10784016	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10784019	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10784034	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10784051	1.00[CEU][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10784059	1.00[CEU][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10877305	0.95[ASN][1000 genomes]
rs10877335	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10877337	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877369	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10877383	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10877410	0.84[ASN][1000 genomes]
rs11173013	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11173257	0.85[ASN][1000 genomes]
rs11173259	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11173260	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11173262	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11173376	0.82[ASN][1000 genomes]
rs11173411	0.87[EUR][1000 genomes]
rs11173440	0.88[JPT][hapmap]
rs11173446	0.89[JPT][hapmap]
rs11173459	0.83[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap]
rs11173494	0.86[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs11173507	0.90[JPT][hapmap]
rs11173541	0.84[JPT][hapmap]
rs11173550	1.00[CEU][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12229203	0.83[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap]
rs12229301	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12229418	0.89[JPT][hapmap]
rs12230687	0.90[JPT][hapmap]
rs12823801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12825223	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4077987	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4129365	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap]
rs4238072	0.93[CEU][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4238073	0.94[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4254134	0.83[CEU][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap]
rs4255599	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4255600	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4312128	0.94[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4322461	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4337105	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4357762	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap]
rs4381428	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4388963	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4391875	0.81[AMR][1000 genomes]
rs4405390	0.93[CEU][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4405391	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4417381	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4417382	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4491316	0.90[MEX][hapmap]
rs4495951	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap]
rs4556618	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4594067	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4767949	0.88[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768168	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.99[ASN][1000 genomes]
rs4768169	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4768170	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57244766	0.84[ASN][1000 genomes]
rs58418587	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58755301	0.84[ASN][1000 genomes]
rs61931208	0.81[AMR][1000 genomes]
rs61933102	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61933154	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6421191	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6421195	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6421196	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6421197	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6421198	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6581250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs6581263	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6581265	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6581266	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6581270	0.83[GIH][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6581271	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6581272	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6581294	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6581357	0.83[CEU][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap]
rs7136929	0.99[ASN][1000 genomes]
rs7296585	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7302849	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7308955	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7485345	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7486196	0.99[ASN][1000 genomes]
rs7486621	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7486631	0.83[CHB][hapmap]
rs7487812	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs7487999	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7952735	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956577	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7959905	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7961070	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7961346	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7964129	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7969282	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7973312	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7980636	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9325166	0.94[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1037457	chr12:39898349-40245401	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv541480	chr12:39898349-40245401	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv899015	chr12:39946354-40118249	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv899017	chr12:39949147-40081619	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv899018	chr12:39949147-40111761	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv899022	chr12:40014427-40111761	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv899023	chr12:40046408-40111761	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
9	nsv899024	chr12:40046408-40188870	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4411336	LRRK2	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40068600-40069800	Enhancers	Primary T cells fromperipheralblood	blood
2	chr12:40068800-40069400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr12:40069000-40069400	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr12:40069200-40069400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr12:40069200-40069800	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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