Variant report

Variant	rs2128276
Chromosome Location	chr12:40430600-40430601
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40428243..40430877-chr12:40432067..40435027,3	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10454013	0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs10506141	0.83[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs10877929	0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs10878029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11174735	0.83[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs11174918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11174998	0.89[ASN][1000 genomes]
rs11175021	0.89[ASN][1000 genomes]
rs11175027	0.83[CHD][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs11175090	0.86[CHD][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs11175094	0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs11175106	0.83[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs11564279	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12228213	0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs1542594	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1871895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2101144	0.88[ASN][1000 genomes]
rs2200085	0.85[JPT][hapmap]
rs2242367	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708445	0.87[ASN][1000 genomes]
rs28370645	0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs28370647	0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs28370666	0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs4533099	0.81[ASN][1000 genomes]
rs61933163	0.81[ASN][1000 genomes]
rs7135815	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs7966741	0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs7967369	0.83[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs7967822	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	nsv1046428	chr12:40226283-40439843	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv541481	chr12:40226283-40439843	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
3	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
4	nsv558597	chr12:40414631-40442892	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2128276	LRRK2	cis	cerebellum	SCAN
rs2128276	SLC2A13	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40394400-40448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:40405400-40445200	Weak transcription	K562	blood
3	chr12:40416600-40441800	Weak transcription	Ovary	ovary
4	chr12:40419000-40447600	Weak transcription	Hela-S3	cervix
5	chr12:40421600-40453400	Weak transcription	Left Ventricle	heart
6	chr12:40426400-40452800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:40428000-40436400	Weak transcription	Fetal Intestine Large	intestine
8	chr12:40428000-40452600	Weak transcription	Fetal Intestine Small	intestine
9	chr12:40429000-40433400	Weak transcription	Fetal Lung	lung
10	chr12:40429400-40441000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:40430000-40433000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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