Variant report

Variant	rs3886747
Chromosome Location	chr12:40761951-40761952
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 126 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10459265	0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs10467144	0.81[CHB][hapmap]
rs10467146	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10735931	0.81[CHB][hapmap]
rs10735934	0.95[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap]
rs10748029	0.94[CHB][hapmap]
rs10748030	0.81[CHB][hapmap]
rs10748033	0.81[CHB][hapmap]
rs10748034	0.81[CHB][hapmap]
rs10784444	0.81[CHB][hapmap]
rs10784461	0.85[CHB][hapmap]
rs10784462	0.85[CHB][hapmap]
rs10784470	0.80[CHB][hapmap]
rs10784486	0.87[CEU][hapmap]
rs10784501	0.81[CHB][hapmap]
rs10784503	0.81[CHB][hapmap]
rs10784504	0.81[CHB][hapmap]
rs10784506	0.83[CHB][hapmap]
rs10784509	0.81[CHB][hapmap]
rs10784518	0.89[ASW][hapmap]
rs10784522	0.86[CHB][hapmap]
rs10784548	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784585	0.83[CEU][hapmap];0.91[JPT][hapmap]
rs10784595	0.81[JPT][hapmap]
rs10784596	0.81[JPT][hapmap]
rs10878245	0.81[CHB][hapmap]
rs10878368	0.81[CHB][hapmap]
rs10878371	0.81[CHB][hapmap]
rs10878377	0.86[JPT][hapmap]
rs10878405	0.90[CHB][hapmap]
rs10878441	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175769	0.85[CHB][hapmap]
rs11175784	0.84[CHB][hapmap]
rs11175845	0.85[CHB][hapmap]
rs11175847	0.85[CHB][hapmap]
rs11175862	0.80[CHB][hapmap]
rs11175911	0.85[CHB][hapmap]
rs11175922	0.85[CHB][hapmap]
rs11176013	0.81[CHB][hapmap]
rs11176030	0.86[CHB][hapmap]
rs11176421	0.80[EUR][1000 genomes]
rs11176495	0.81[JPT][hapmap]
rs11564148	0.86[CHB][hapmap]
rs12146857	0.81[CHB][hapmap]
rs12314982	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12367542	0.86[CHB][hapmap]
rs12369882	0.85[CHB][hapmap]
rs12426362	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12820920	0.85[CHB][hapmap]
rs1365765	0.89[ASW][hapmap]
rs1365770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1427264	0.81[CHB][hapmap]
rs1427265	0.81[CHB][hapmap]
rs1427266	0.81[CHB][hapmap]
rs1427271	0.89[ASW][hapmap]
rs1444221	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1465528	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1491938	0.85[CHB][hapmap]
rs17443815	0.85[CHB][hapmap]
rs17444124	0.90[CHB][hapmap]
rs17466605	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17519846	0.85[CHB][hapmap]
rs1820545	0.81[JPT][hapmap]
rs1896252	0.81[CHB][hapmap]
rs1896253	0.81[CHB][hapmap]
rs1896254	0.81[CHB][hapmap]
rs2081700	0.87[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2081701	0.87[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2114568	0.81[CHB][hapmap]
rs2162469	0.81[CHB][hapmap]
rs2404580	0.81[CHB][hapmap]
rs2404840	0.81[JPT][hapmap]
rs2896982	0.91[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3761863	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789328	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789330	0.89[ASW][hapmap]
rs3906483	0.88[EUR][1000 genomes]
rs4272849	0.81[CHB][hapmap]
rs4280068	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4310676	0.87[CEU][hapmap]
rs4351885	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4483664	0.87[CEU][hapmap]
rs4767969	0.81[CHB][hapmap]
rs4767973	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4768229	0.81[CHB][hapmap]
rs4768230	0.86[CHB][hapmap]
rs4768233	0.89[ASW][hapmap]
rs4768234	0.89[ASW][hapmap]
rs4768236	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768237	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5010412	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581667	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs6581668	0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap]
rs7134408	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137160	0.81[CHB][hapmap]
rs7137809	0.81[JPT][hapmap]
rs721711	0.81[CHB][hapmap]
rs721712	0.81[CHB][hapmap]
rs721713	0.81[CHB][hapmap]
rs7298930	0.81[CHB][hapmap]
rs7302841	0.85[CHB][hapmap]
rs7307276	0.81[CHB][hapmap]
rs7307562	0.84[CHB][hapmap];0.80[JPT][hapmap]
rs7308193	0.87[CEU][hapmap]
rs7308560	0.81[JPT][hapmap]
rs7309197	0.85[CHB][hapmap]
rs7310390	0.91[CEU][hapmap];0.95[JPT][hapmap]
rs7954300	0.91[CEU][hapmap]
rs7954318	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7957057	0.87[CEU][hapmap]
rs7957754	0.85[CHB][hapmap]
rs7968048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968721	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7972535	0.81[JPT][hapmap]
rs7973058	0.86[CHB][hapmap]
rs7973479	0.85[CHB][hapmap]
rs7975124	0.91[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7976715	0.88[ASN][1000 genomes]
rs954884	0.81[CHB][hapmap]
rs963243	0.86[JPT][hapmap]
rs994798	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv832377	chr12:40704881-40855223	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv899032	chr12:40735939-40827479	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv558598	chr12:40742363-40828264	Strong transcription Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv899033	chr12:40758652-41122288	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3886747	LRRK2	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40640600-40768200	Weak transcription	Pancreas	Pancrea
2	chr12:40681200-40763000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:40687200-40765000	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr12:40726200-40766600	Weak transcription	A549	lung
5	chr12:40726200-40767800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:40732800-40764000	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:40747200-40762400	Strong transcription	Primary B cells from peripheral blood	blood
8	chr12:40747800-40765000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr12:40747800-40765200	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr12:40751400-40762600	Strong transcription	Liver	Liver
11	chr12:40751800-40763600	Weak transcription	Brain Anterior Caudate	brain
12	chr12:40754000-40762000	Strong transcription	Primary B cells from cord blood	blood
13	chr12:40754800-40764000	Weak transcription	Esophagus	oesophagus
14	chr12:40754800-40765600	Weak transcription	Aorta	Aorta
15	chr12:40754800-40767600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr12:40756000-40763600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:40758200-40765600	Weak transcription	Adipose Nuclei	Adipose
18	chr12:40759000-40765200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:40759200-40764000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr12:40760000-40765600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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