Variant report

Variant	rs6581357
Chromosome Location	chr12:40205999-40206000
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40205089..40207164-chr12:40209269..40211220,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10219652	0.82[CEU][hapmap]
rs10444570	0.81[MEX][hapmap];0.83[TSI][hapmap]
rs10735885	0.83[CEU][hapmap]
rs10747878	0.81[CEU][hapmap]
rs10783959	0.83[CEU][hapmap]
rs10784001	0.81[MEX][hapmap]
rs10784051	0.83[CEU][hapmap]
rs10784059	0.83[CEU][hapmap]
rs10784065	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877383	0.83[CEU][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs10877474	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11173459	0.81[MEX][hapmap]
rs11173494	0.90[MEX][hapmap]
rs11173550	0.83[CEU][hapmap]
rs12229203	0.81[MEX][hapmap]
rs12823801	0.83[CEU][hapmap]
rs4129365	0.81[MEX][hapmap]
rs4238073	0.81[MEX][hapmap];0.83[TSI][hapmap]
rs4254134	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4357762	0.81[MEX][hapmap]
rs4372520	1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4393383	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4411336	0.83[CEU][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap]
rs4491316	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.80[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4495951	0.81[MEX][hapmap]
rs4545632	0.91[ASN][1000 genomes]
rs4594067	0.81[MEX][hapmap]
rs4767949	0.82[MEX][hapmap];0.82[TSI][hapmap]
rs4768168	0.81[MEX][hapmap]
rs6421196	0.81[MEX][hapmap]
rs6581250	0.83[CEU][hapmap]
rs6581271	0.81[MEX][hapmap]
rs6581351	0.88[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs7135877	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7136860	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73092111	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73092113	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73092119	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7487812	0.87[CEU][hapmap]

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	nsv1037457	chr12:39898349-40245401	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv541480	chr12:39898349-40245401	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1052012	chr12:40180398-40237782	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1040628	chr12:40180398-40244001	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv899025	chr12:40191778-40321846	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv1049214	chr12:40197549-40326495	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6581357	LRRK2	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40193800-40255800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:40194600-40232600	Weak transcription	Right Ventricle	heart
3	chr12:40199200-40265400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:40205800-40206200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain

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