Variant report

Variant	rs10878123
Chromosome Location	chr12:40532533-40532534
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40526853..40529105-chr12:40530805..40532717,2	MCF-7	breast:
2	12:40525880-40532672..12:40703633-40711447	GM12878	blood:

Variant related genes	Relation type
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10506148	0.85[CHB][hapmap]
rs10784340	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs10877913	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[MEX][hapmap];0.84[EUR][1000 genomes]
rs10877955	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10877971	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10878208	0.83[JPT][hapmap]
rs11174831	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11174928	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs11175102	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11175103	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs11175256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11175260	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11175332	0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11175371	0.86[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs11175401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11175405	0.89[JPT][hapmap]
rs11175422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11175458	0.85[ASN][1000 genomes]
rs11175540	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11175558	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs11564115	1.00[JPT][hapmap]
rs12372213	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12581285	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1388596	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs1472117	1.00[JPT][hapmap]
rs1491924	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1491939	0.84[JPT][hapmap]
rs1491942	0.95[JPT][hapmap]
rs17442157	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17443199	0.85[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs17458156	0.86[EUR][1000 genomes]
rs17458613	1.00[CEU][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17461429	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17518546	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2046931	0.90[JPT][hapmap]
rs2131088	1.00[JPT][hapmap]
rs2201144	1.00[ASW][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap]
rs2253736	0.88[ASN][1000 genomes]
rs2638224	0.84[ASN][1000 genomes]
rs2638244	0.90[JPT][hapmap]
rs2638250	0.80[ASN][1000 genomes]
rs2638268	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2638270	0.86[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2638271	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2708437	1.00[ASW][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap]
rs2708438	1.00[ASW][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap]
rs2708463	0.80[ASN][1000 genomes]
rs2708478	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2723269	1.00[JPT][hapmap]
rs28365172	0.86[EUR][1000 genomes]
rs28365179	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28365683	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs28370683	0.86[EUR][1000 genomes]
rs72644819	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7310104	0.90[JPT][hapmap]
rs949640	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	esv1836585	chr12:40492814-40540939	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv1839483	chr12:40492814-40540939	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv899030	chr12:40509341-40580440	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv899031	chr12:40520684-40580440	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10878123	LRRK2	cis	Liver	GTEx
rs10878123	LRRK2	cis	multi-tissue	Pritchard

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40531400-40532600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:40531400-40532600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:40531400-40532600	Enhancers	NHEK	skin
4	chr12:40531600-40532800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:40531800-40532800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:40532400-40535600	Weak transcription	HMEC	breast

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