Variant report

Variant	rs10784585
Chromosome Location	chr12:40786804-40786805
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1019709	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs10467146	0.83[CEU][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs10784486	0.95[CEU][hapmap];0.84[TSI][hapmap]
rs10784548	0.83[CEU][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs10784589	0.82[ASN][1000 genomes]
rs10784595	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs10784596	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs10878377	0.86[JPT][hapmap]
rs10878441	0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs10878507	0.94[ASN][1000 genomes]
rs11176421	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176495	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs12314982	0.91[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12426362	0.83[CEU][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs1365770	0.81[EUR][1000 genomes]
rs1427263	0.86[CEU][hapmap]
rs1427267	0.87[CEU][hapmap]
rs1444221	0.81[EUR][1000 genomes]
rs1465528	0.81[EUR][1000 genomes]
rs17466605	0.83[CEU][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs1820544	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1820545	0.82[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs2069228	0.87[CEU][hapmap]
rs2081700	0.95[CEU][hapmap];0.94[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2081701	0.95[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2404840	0.83[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2896975	0.87[CEU][hapmap]
rs2896982	0.91[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3761863	0.83[CEU][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs3789328	0.80[EUR][1000 genomes]
rs3886747	0.83[CEU][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs3906483	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4280068	0.91[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4310676	0.95[CEU][hapmap]
rs4351885	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4483664	0.95[CEU][hapmap]
rs4767973	0.83[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs4768224	0.86[CEU][hapmap];0.81[TSI][hapmap]
rs4768236	0.83[CEU][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs4768237	0.83[CEU][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs5010412	0.81[EUR][1000 genomes]
rs7134408	0.83[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs7137665	0.87[CEU][hapmap]
rs7137809	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs721709	0.87[CEU][hapmap]
rs7302503	0.87[CEU][hapmap]
rs7308193	0.95[CEU][hapmap]
rs7308560	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7310390	0.91[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs7954300	0.91[CEU][hapmap]
rs7954318	0.91[CEU][hapmap];0.97[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7957057	0.95[CEU][hapmap];0.84[TSI][hapmap]
rs7968048	0.81[EUR][1000 genomes]
rs7968721	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7972535	0.81[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7975124	0.91[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs963243	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs994798	0.83[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832377	chr12:40704881-40855223	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv899032	chr12:40735939-40827479	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv558598	chr12:40742363-40828264	Strong transcription Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv899033	chr12:40758652-41122288	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv1047639	chr12:40774370-40804386	Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10784585	LRRK2	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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