Variant report

Variant	rs1482282
Chromosome Location	chr12:40482052-40482053
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:40480723..40487168-chr12:40489659..40495663,7	K562	blood:
2	chr12:40480335..40482616-chr12:40490447..40492552,2	MCF-7	breast:
3	chr12:40481786..40484578-chr12:40492831..40495668,2	MCF-7	breast:
4	chr12:40478482..40480663-chr12:40481421..40484352,2	MCF-7	breast:
5	chr12:40481016..40484666-chr12:40485206..40488003,4	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10506145	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1086490	1.00[JPT][hapmap]
rs10877837	1.00[JPT][hapmap]
rs11174370	1.00[JPT][hapmap]
rs11564133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564137	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11564139	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11564160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11564194	1.00[JPT][hapmap];0.86[MEX][hapmap]
rs11564223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11564282	1.00[JPT][hapmap]
rs12312535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12371119	1.00[JPT][hapmap]
rs12810368	1.00[JPT][hapmap]
rs12827948	1.00[JPT][hapmap]
rs1491926	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17442108	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17442304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17442469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17442749	1.00[JPT][hapmap]
rs17442756	1.00[JPT][hapmap]
rs17442805	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17442853	1.00[JPT][hapmap]
rs17443112	1.00[JPT][hapmap];0.93[AFR][1000 genomes]
rs17458299	0.84[CEU][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17458396	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17458403	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17461082	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17461492	0.93[AFR][1000 genomes]
rs17465400	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17465519	0.85[AFR][1000 genomes]
rs17465540	0.85[AFR][1000 genomes]
rs17483628	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];0.96[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17559478	1.00[JPT][hapmap]
rs2046929	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2086598	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2404346	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2404574	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2708404	1.00[JPT][hapmap]
rs28370607	1.00[JPT][hapmap]
rs28370644	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28370654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28370656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28370659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28370681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28370805	1.00[JPT][hapmap]
rs28740188	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55707305	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55993200	0.93[AFR][1000 genomes]
rs7305377	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306718	1.00[JPT][hapmap]
rs7484475	1.00[JPT][hapmap]
rs7969495	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];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7974522	1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs7974972	1.00[JPT][hapmap]
rs992851	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv899028	chr12:40478652-40524180	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv899029	chr12:40478652-40536061	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1482282	LRRK2	cis	cerebellum	SCAN
rs1482282	LRRK2	cis	parietal	SCAN
rs1482282	BOP1	trans	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40453800-40487400	Weak transcription	Left Ventricle	heart
2	chr12:40464400-40493200	Weak transcription	Colon Smooth Muscle	Colon
3	chr12:40466400-40498200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:40471400-40496800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr12:40474400-40497000	Weak transcription	Ovary	ovary
6	chr12:40475400-40483000	Weak transcription	Adipose Nuclei	Adipose
7	chr12:40475400-40497200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:40475600-40496400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:40476200-40485400	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr12:40476400-40486200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr12:40476400-40492400	Weak transcription	K562	blood
12	chr12:40476400-40497400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:40476600-40484600	Weak transcription	Fetal Intestine Large	intestine
14	chr12:40476600-40492600	Weak transcription	Lung	lung
15	chr12:40476600-40498400	Weak transcription	Fetal Stomach	stomach
16	chr12:40476800-40497800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:40477000-40492000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:40477000-40497000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr12:40477200-40495200	Weak transcription	Hela-S3	cervix
20	chr12:40477400-40496800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr12:40478600-40492600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr12:40479000-40493400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr12:40479200-40493200	Weak transcription	Fetal Heart	heart
24	chr12:40480200-40493400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:40480600-40485800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:40480600-40496800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:40481200-40492800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:40481400-40482400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:40482000-40482400	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr12:40482000-40497800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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