Variant report

Variant	rs17443199
Chromosome Location	chr12:40586433-40586434
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP1	chr12:40586382-40587148	GM12878	blood:	n/a	n/a
2	RELA	chr12:40586393-40587378	GM12891	blood:	n/a	n/a
3	FOXM1	chr12:40586404-40587183	GM12878	blood:	n/a	n/a
4	IKZF1	chr12:40586419-40587024	GM12878	blood:	n/a	n/a
5	FOXM1	chr12:40586416-40587137	GM12878	blood:	n/a	n/a
6	ZNF384	chr12:40585946-40587130	GM12878	blood:	n/a	n/a
7	RELA	chr12:40586366-40587301	GM12878	blood:	n/a	n/a
8	SPI1	chr12:40586351-40586862	HL-60	blood:	n/a	n/a
9	MTA3	chr12:40586401-40587222	GM12878	blood:	n/a	n/a
10	RELA	chr12:40586253-40587360	GM18951	blood:	n/a	n/a
11	PAX5	chr12:40586410-40587177	GM12878	blood:	n/a	chr12:40586893-40586912
12	EBF1	chr12:40586394-40587108	GM12878	blood:	n/a	n/a
13	MAX	chr12:40586370-40586893	GM12878	blood:	n/a	n/a
14	RELA	chr12:40586374-40587289	GM19099	blood:	n/a	n/a
15	EP300	chr12:40586294-40587217	GM12878	blood:	n/a	n/a
16	MEF2A	chr12:40586387-40587187	GM12878	blood:	n/a	n/a
17	RCOR1	chr12:40586329-40587132	GM12878	blood:	n/a	n/a
18	ATF2	chr12:40586412-40587192	GM12878	blood:	n/a	n/a
19	ATF2	chr12:40586416-40587052	GM12878	blood:	n/a	n/a
20	RUNX3	chr12:40586380-40587138	GM12878	blood:	n/a	n/a
21	NFIC	chr12:40586156-40587180	GM12878	blood:	n/a	n/a
22	MXI1	chr12:40586282-40587213	GM12878	blood:	n/a	n/a
23	SPI1	chr12:40586252-40587283	GM12878	blood:	n/a	n/a
24	BCLAF1	chr12:40586427-40586922	GM12878	blood:	n/a	n/a
25	CHD2	chr12:40586158-40587275	GM12878	blood:	n/a	n/a
26	TBL1XR1	chr12:40586180-40587326	GM12878	blood:	n/a	n/a
27	RUNX3	chr12:40586309-40587128	GM12878	blood:	n/a	n/a
28	NFIC	chr12:40586300-40587223	GM12878	blood:	n/a	n/a
29	TBP	chr12:40586355-40587139	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
LRRK2	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10878123	0.85[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs10878208	0.81[CHB][hapmap];0.89[ASN][1000 genomes]
rs11175256	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs11175260	0.82[ASN][1000 genomes]
rs11175332	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11175371	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11175401	0.86[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs11175405	0.95[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11175422	0.85[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs11175458	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175540	0.96[ASN][1000 genomes]
rs11175558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11564115	0.89[JPT][hapmap]
rs12581617	0.86[ASN][1000 genomes]
rs1388593	0.82[ASN][1000 genomes]
rs1472117	0.89[JPT][hapmap]
rs1491922	0.89[ASN][1000 genomes]
rs1491923	0.89[ASN][1000 genomes]
rs1491924	0.85[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs1491925	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1491942	0.83[JPT][hapmap]
rs17461429	0.93[ASN][1000 genomes]
rs1907630	0.82[ASN][1000 genomes]
rs1907631	0.82[ASN][1000 genomes]
rs2046931	0.87[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs2131088	0.89[JPT][hapmap]
rs2172240	0.82[ASN][1000 genomes]
rs2172241	0.82[ASN][1000 genomes]
rs2201144	0.89[JPT][hapmap]
rs2638244	0.90[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs2638247	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2638250	0.84[ASN][1000 genomes]
rs2638268	0.81[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs2638269	0.84[ASN][1000 genomes]
rs2638270	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2638271	0.80[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2708426	0.82[ASN][1000 genomes]
rs2708437	0.89[JPT][hapmap]
rs2708438	0.89[JPT][hapmap]
rs2708463	0.84[ASN][1000 genomes]
rs2708465	0.87[ASN][1000 genomes]
rs2708478	0.84[ASN][1000 genomes]
rs2723260	0.82[ASN][1000 genomes]
rs2723269	0.89[JPT][hapmap]
rs28365179	0.82[CHB][hapmap]
rs72644819	0.96[ASN][1000 genomes]
rs7310104	0.87[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs949640	0.85[CHB][hapmap];0.89[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	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	nsv1045516	chr12:40543200-40589557	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
3	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17443199	LRRK2	cis	Muscle Skeletal	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40585600-40587200	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr12:40585800-40587000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:40585800-40587200	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr12:40585800-40587400	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr12:40586000-40586800	Enhancers	Primary B cells from cord blood	blood
6	chr12:40586000-40586800	Enhancers	Primary B cells from peripheral blood	blood
7	chr12:40586000-40587000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:40586000-40587000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr12:40586000-40587400	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr12:40586000-40587600	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr12:40586000-40591000	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr12:40586200-40586600	Enhancers	Primary T cells from cord blood	blood
13	chr12:40586200-40586800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:40586200-40586800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:40586200-40587000	Active TSS	GM12878-XiMat	blood
16	chr12:40586200-40587200	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr12:40586200-40591600	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr12:40586400-40587000	Enhancers	Primary hematopoietic stem cells	blood
19	chr12:40586400-40587000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr12:40586400-40587200	Enhancers	HUVEC	blood vessel

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