Variant report

Variant	rs1512941
Chromosome Location	chr12:39768356-39768357
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:39768164..39770883-chr12:39771123..39773923,3	K562	blood:
2	chr12:39764517..39769063-chr12:39834166..39838574,6	K562	blood:
3	chr12:39762097..39763744-chr12:39766808..39769516,2	MCF-7	breast:
4	chr12:39766807..39768997-chr12:39769052..39771333,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252974	Chromatin interaction
ENSG00000139116	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11172144	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11172162	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs12227286	1.00[JPT][hapmap]
rs12228013	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs1512943	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17126997	0.81[CEU][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17127029	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17127070	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17127094	0.84[CEU][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17127100	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17127129	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.83[ASN][1000 genomes]
rs17127138	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.83[ASN][1000 genomes]
rs2137495	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2271478	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2292491	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736466	0.81[ASW][hapmap]
rs4294600	0.93[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs4620763	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57196300	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58891998	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59967849	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61039034	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7135918	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307730	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7308138	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73086885	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088816	0.83[ASN][1000 genomes]
rs7309234	0.93[CEU][hapmap];0.90[JPT][hapmap]
rs7312611	0.90[JPT][hapmap]
rs7956823	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7966841	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970819	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970944	0.83[ASN][1000 genomes]
rs7974928	0.81[ASW][hapmap]
rs7976275	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7980595	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs963637	0.81[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	nsv832375	chr12:39599362-39784722	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv832376	chr12:39633080-39808277	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv558589	chr12:39667861-39768356	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1512941	LRRK2	cis	parietal	SCAN
rs1512941	ABCD2	cis	multi-tissue	Pritchard

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39697800-39771800	Weak transcription	Fetal Kidney	kidney
2	chr12:39721000-39770600	Weak transcription	Gastric	stomach
3	chr12:39727000-39779200	Weak transcription	Aorta	Aorta
4	chr12:39745000-39778600	Weak transcription	Pancreas	Pancrea
5	chr12:39751400-39770400	Weak transcription	Brain Hippocampus Middle	brain
6	chr12:39751600-39771800	Weak transcription	Brain Anterior Caudate	brain
7	chr12:39752200-39769000	Weak transcription	Ovary	ovary
8	chr12:39752200-39769200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:39757000-39784600	Weak transcription	Brain Germinal Matrix	brain
10	chr12:39758600-39770600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr12:39761200-39769000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr12:39761800-39806000	Weak transcription	Hela-S3	cervix
13	chr12:39762800-39771200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr12:39763000-39781400	Weak transcription	A549	lung
15	chr12:39763800-39768400	Weak transcription	Fetal Brain Female	brain
16	chr12:39764000-39769200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:39764000-39781000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:39765800-39772200	Weak transcription	Left Ventricle	heart
19	chr12:39766600-39769800	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr12:39767400-39770800	Weak transcription	Right Ventricle	heart
21	chr12:39767400-39784800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:39767600-39769400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr12:39767600-39791400	Weak transcription	GM12878-XiMat	blood
24	chr12:39767800-39769000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr12:39767800-39769000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr12:39767800-39769000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr12:39767800-39769200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr12:39767800-39769200	Weak transcription	Fetal Heart	heart
29	chr12:39767800-39771000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:39767800-39784800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:39768000-39769200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr12:39768000-39776800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:39768200-39769200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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