Variant report

Variant	rs7310178
Chromosome Location	chr12:39971240-39971241
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10877173	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10877201	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs11172144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs11172162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs11172366	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11172480	0.86[ASN][1000 genomes]
rs11172488	0.83[ASN][1000 genomes]
rs11172616	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172645	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172646	0.92[ASN][1000 genomes]
rs11172647	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172650	0.86[AFR][1000 genomes]
rs11172687	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172692	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172697	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172713	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs11172722	0.83[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs11172794	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11172848	0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11172896	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11172897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12227286	0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12227668	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12228013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs12228617	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs12229160	0.97[EUR][1000 genomes]
rs12229370	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12230055	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17127094	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs17127129	0.93[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs17127138	0.86[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs35790935	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35858791	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4072006	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4285917	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4294600	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4298947	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4639970	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57847223	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58036566	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59518553	0.92[ASN][1000 genomes]
rs59528535	0.92[ASN][1000 genomes]
rs61258856	0.95[EUR][1000 genomes]
rs6581188	0.87[AFR][1000 genomes]
rs6581228	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs7133376	0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7133599	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7294474	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7302302	0.95[EUR][1000 genomes]
rs73088816	0.95[EUR][1000 genomes]
rs7309234	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73094447	0.95[EUR][1000 genomes]
rs73094449	0.95[EUR][1000 genomes]
rs73094488	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7310871	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7312611	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs73268358	0.92[ASN][1000 genomes]
rs73268359	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74086536	0.95[EUR][1000 genomes]
rs7966841	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs7970944	0.95[EUR][1000 genomes]
rs7976275	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv1039645	chr12:39903123-40022029	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats 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	5 gene(s)	inside rSNPs	diseases
5	nsv522940	chr12:39946354-39998144	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv469359	chr12:39946354-40034699	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv558591	chr12:39946354-40034699	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv469361	chr12:39946354-40042220	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv558592	chr12:39946354-40042220	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv899014	chr12:39946354-40068896	Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription 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	2 gene(s)	inside rSNPs	diseases
11	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
12	nsv899016	chr12:39949147-40004906	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
13	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
14	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
15	nsv899019	chr12:39955802-40004906	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7310178	LRRK2	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39948800-40000000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr12:39953800-39978600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr12:39962600-39974200	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr12:39963200-39975600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr12:39963400-39991600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:39963600-39972000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:39963600-39978200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr12:39963800-40010200	Weak transcription	Left Ventricle	heart
9	chr12:39964400-39979000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr12:39965400-39973600	Weak transcription	Adipose Nuclei	Adipose
11	chr12:39966600-39993200	Weak transcription	GM12878-XiMat	blood
12	chr12:39966600-39993400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr12:39966800-40009400	Weak transcription	Primary T cells from cord blood	blood
14	chr12:39967400-39978400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr12:39967800-39993200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr12:39969000-39973600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:39969400-39977400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:39969800-39975000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:39969800-39977800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:39970000-39972400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr12:39970200-39978800	Weak transcription	Fetal Brain Female	brain
22	chr12:39970400-39978200	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr12:39970400-39981000	Weak transcription	Fetal Brain Male	brain
24	chr12:39971000-39972800	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr12:39971200-39974800	Strong transcription	Primary T helper cells fromperipheralblood	blood

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