Variant report

Variant	rs17127129
Chromosome Location	chr12:39825613-39825614
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:39825307..39826136-chr12:39836786..39837540,3	MCF-7	breast:
2	chr12:39825464..39827632-chr12:39834768..39838151,3	MCF-7	breast:
3	chr12:39825423..39826136-chr12:39836842..39837540,2	MCF-7	breast:
4	chr12:39775530..39777936-chr12:39825264..39827786,2	K562	blood:

Variant related genes	Relation type
ENSG00000139116	Chromatin interaction
ENSG00000252974	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10877173	1.00[JPT][hapmap]
rs10877201	0.90[JPT][hapmap]
rs11172144	0.93[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11172162	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11172366	0.95[EUR][1000 genomes]
rs11172616	0.95[EUR][1000 genomes]
rs11172645	0.95[EUR][1000 genomes]
rs11172647	0.95[EUR][1000 genomes]
rs11172687	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs11172692	0.95[EUR][1000 genomes]
rs11172697	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11172713	0.90[JPT][hapmap]
rs11172722	0.90[JPT][hapmap]
rs11172794	1.00[JPT][hapmap]
rs11172848	1.00[JPT][hapmap]
rs11172896	0.81[EUR][1000 genomes]
rs11172897	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12227286	1.00[JPT][hapmap]
rs12227668	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12228013	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12228617	0.90[JPT][hapmap]
rs12229160	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12229370	0.97[EUR][1000 genomes]
rs12230055	0.97[EUR][1000 genomes]
rs1512941	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]
rs1512943	0.83[ASN][1000 genomes]
rs17126997	0.86[CEU][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs17127029	0.83[ASN][1000 genomes]
rs17127070	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs17127094	0.92[CEU][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs17127100	0.83[ASN][1000 genomes]
rs17127138	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271478	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2292491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs35790935	0.97[EUR][1000 genomes]
rs35858791	0.97[EUR][1000 genomes]
rs4072006	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4285917	0.96[EUR][1000 genomes]
rs4294600	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs4298947	0.91[EUR][1000 genomes]
rs4639970	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57196300	0.83[ASN][1000 genomes]
rs57847223	0.95[EUR][1000 genomes]
rs58036566	0.95[EUR][1000 genomes]
rs59967849	0.83[ASN][1000 genomes]
rs61258856	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6581228	0.90[JPT][hapmap]
rs7133376	0.90[JPT][hapmap]
rs7133599	0.95[EUR][1000 genomes]
rs7135918	0.83[ASN][1000 genomes]
rs7294474	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7302302	1.00[EUR][1000 genomes]
rs7308138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs73086885	0.83[ASN][1000 genomes]
rs73088816	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309234	1.00[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73094447	1.00[EUR][1000 genomes]
rs73094449	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73094488	0.97[EUR][1000 genomes]
rs7310178	0.93[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs7310871	0.95[EUR][1000 genomes]
rs7312611	0.90[JPT][hapmap]
rs73268359	0.81[EUR][1000 genomes]
rs74086536	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7956823	0.82[ASN][1000 genomes]
rs7966841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7970819	0.83[ASN][1000 genomes]
rs7970944	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976275	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs7978854	0.83[ASN][1000 genomes]
rs7980595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs7980857	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17127129	LRRK2	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39785000-39829200	Weak transcription	K562	blood
2	chr12:39806600-39834200	Weak transcription	Hela-S3	cervix
3	chr12:39808600-39830800	Weak transcription	Fetal Brain Female	brain
4	chr12:39813600-39833400	Weak transcription	Brain Germinal Matrix	brain
5	chr12:39814200-39825800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr12:39814400-39833800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:39816000-39834000	Weak transcription	Left Ventricle	heart
8	chr12:39821400-39835600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr12:39822000-39829800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr12:39822200-39832200	Weak transcription	A549	lung
11	chr12:39822200-39833000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:39823000-39826000	Enhancers	Liver	Liver
13	chr12:39823600-39829400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:39824000-39832400	Weak transcription	HepG2	liver
15	chr12:39824400-39826000	Enhancers	Fetal Heart	heart
16	chr12:39824600-39826000	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr12:39824600-39826800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:39825000-39827200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:39825200-39825800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr12:39825200-39827800	Weak transcription	Right Ventricle	heart
21	chr12:39825200-39835600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:39825400-39826200	Enhancers	Pancreatic Islets	Pancreatic Islet
23	chr12:39825400-39834600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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