Variant report

Variant	rs12810368
Chromosome Location	chr12:40367171-40367172
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	12:40355227-40369361..12:40703633-40711447	GM12878	blood:
2	chr12:40366212..40368701-chr12:40371213..40373110,2	K562	blood:

Variant related genes	Relation type
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10506145	1.00[JPT][hapmap]
rs1086490	1.00[JPT][hapmap]
rs10877837	1.00[JPT][hapmap]
rs10877867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11174370	1.00[JPT][hapmap]
rs11564133	1.00[JPT][hapmap]
rs11564139	1.00[JPT][hapmap]
rs11564160	1.00[JPT][hapmap]
rs11564194	1.00[JPT][hapmap]
rs11564221	0.88[CHB][hapmap];0.85[ASN][1000 genomes]
rs11564223	1.00[JPT][hapmap]
rs11564282	1.00[JPT][hapmap]
rs12312535	1.00[JPT][hapmap]
rs12371119	1.00[JPT][hapmap]
rs12827948	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1319734	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs1482282	1.00[JPT][hapmap]
rs17442108	1.00[JPT][hapmap]
rs17442304	1.00[JPT][hapmap]
rs17442469	1.00[JPT][hapmap]
rs17442749	1.00[JPT][hapmap]
rs17442756	1.00[JPT][hapmap]
rs17442853	1.00[JPT][hapmap]
rs17461082	1.00[JPT][hapmap]
rs17483628	1.00[JPT][hapmap]
rs17559478	1.00[JPT][hapmap]
rs2046929	1.00[JPT][hapmap]
rs2404574	1.00[JPT][hapmap]
rs28370607	1.00[JPT][hapmap]
rs28370644	1.00[JPT][hapmap]
rs28370654	1.00[JPT][hapmap]
rs28370656	1.00[JPT][hapmap]
rs28370659	1.00[JPT][hapmap]
rs28370681	1.00[JPT][hapmap]
rs28370805	1.00[JPT][hapmap]
rs4399379	1.00[JPT][hapmap]
rs7306718	1.00[JPT][hapmap]
rs7311756	0.85[ASN][1000 genomes]
rs73280629	0.95[ASN][1000 genomes]
rs7484475	1.00[JPT][hapmap]
rs7966222	0.81[GIH][hapmap]
rs7969495	1.00[JPT][hapmap]
rs7974972	1.00[JPT][hapmap]
rs7976837	0.86[LWK][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	nsv1046428	chr12:40226283-40439843	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv541481	chr12:40226283-40439843	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1052202	chr12:40322607-40406760	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12810368	LRRK2	cis	cerebellum	SCAN
rs12810368	CYTSB	trans	cerebellum	SCAN
rs12810368	ZDHHC13	trans	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40347800-40369800	Weak transcription	Pancreas	Pancrea
2	chr12:40363000-40369800	Weak transcription	Psoas Muscle	Psoas
3	chr12:40364400-40391400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:40366400-40371800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr12:40366400-40390200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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