Variant report

Variant	rs11564279
Chromosome Location	chr12:40445759-40445760
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	12:40441273-40454218..12:40703633-40711447	GM12878	blood:
2	chr12:40443219..40446244-chr12:40497398..40500179,3	MCF-7	breast:
3	chr12:40445246..40446962-chr12:40448695..40451443,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188906	Chromatin interaction
ENSG00000151229	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10454013	0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs10506141	0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs10877929	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs10878029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878258	0.82[YRI][hapmap]
rs11174735	0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs11174918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11174998	0.90[ASN][1000 genomes]
rs11175021	0.90[ASN][1000 genomes]
rs11175027	0.86[CHD][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs11175090	0.83[CHD][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs11175094	0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs11175106	0.86[CHD][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs12228213	0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs1542594	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1871895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2101144	0.89[ASN][1000 genomes]
rs2128276	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]
rs2200085	0.85[JPT][hapmap]
rs2242367	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708445	0.88[ASN][1000 genomes]
rs28370645	0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs28370647	0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs28370666	0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs4533099	0.82[ASN][1000 genomes]
rs61933163	0.82[ASN][1000 genomes]
rs7134379	0.82[YRI][hapmap]
rs7135815	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs7966741	0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs7967369	0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs7967822	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[EUR][1000 genomes];0.99[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11564279	LRRK2	cis	cerebellum	SCAN
rs11564279	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	chr12:40419000-40447600	Weak transcription	Hela-S3	cervix
3	chr12:40421600-40453400	Weak transcription	Left Ventricle	heart
4	chr12:40426400-40452800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:40428000-40452600	Weak transcription	Fetal Intestine Small	intestine
6	chr12:40442200-40447600	Weak transcription	A549	lung
7	chr12:40442200-40451400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:40444000-40453400	Weak transcription	Right Ventricle	heart
9	chr12:40444400-40447600	Weak transcription	Colon Smooth Muscle	Colon
10	chr12:40445000-40448400	Weak transcription	Fetal Stomach	stomach
11	chr12:40445000-40448600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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