Variant report

Variant	rs10877201
Chromosome Location	chr12:40012297-40012298
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	chr12:40006374..40007995-chr12:40011197..40013165,2	K562	blood:
2	chr12:40010562..40012556-chr12:40014262..40016328,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10877173	0.90[JPT][hapmap]
rs11172144	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs11172162	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs11172687	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs11172713	0.80[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172722	0.87[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172794	0.90[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11172848	0.90[JPT][hapmap]
rs11172896	0.82[ASN][1000 genomes]
rs11172897	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs12227286	0.90[JPT][hapmap]
rs12227668	0.81[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs12228013	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs12228617	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12231004	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17127129	0.90[JPT][hapmap]
rs17127138	0.89[JPT][hapmap]
rs4072006	0.81[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs4294600	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs59528535	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6581228	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7133376	0.80[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7134015	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7307784	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7310178	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs7312611	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs73268358	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73268359	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv1039645	chr12:39903123-40022029	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats 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	5 gene(s)	inside rSNPs	diseases
5	nsv469359	chr12:39946354-40034699	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv558591	chr12:39946354-40034699	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv469361	chr12:39946354-40042220	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv558592	chr12:39946354-40042220	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv899014	chr12:39946354-40068896	Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription 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	2 gene(s)	inside rSNPs	diseases
10	nsv899015	chr12:39946354-40118249	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats 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	2 gene(s)	inside rSNPs	diseases
11	nsv899017	chr12:39949147-40081619	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
12	nsv899018	chr12:39949147-40111761	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
13	nsv899020	chr12:39985206-40040331	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv899021	chr12:39989172-40053423	Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10877201	LRRK2	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40006800-40015000	Active TSS	GM12878-XiMat	blood
2	chr12:40007600-40012400	Active TSS	Adipose Nuclei	Adipose
3	chr12:40008000-40012600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:40009400-40012400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
5	chr12:40009400-40015400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr12:40009600-40014800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:40009600-40015000	Active TSS	Primary T killer memory cells from peripheral blood	blood
8	chr12:40009800-40014800	Active TSS	Brain Angular Gyrus	brain
9	chr12:40009800-40015000	Active TSS	Primary T cells fromperipheralblood	blood
10	chr12:40009800-40015000	Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr12:40009800-40015200	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr12:40009800-40015200	Active TSS	Right Atrium	heart
13	chr12:40010000-40012400	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr12:40010000-40012600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:40010000-40012600	Active TSS	Stomach Smooth Muscle	stomach
16	chr12:40010000-40012800	Active TSS	Duodenum Mucosa	Duodenum
17	chr12:40010200-40014600	Active TSS	Brain Germinal Matrix	brain
18	chr12:40010400-40012400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:40010800-40012400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr12:40010800-40012400	Weak transcription	Colonic Mucosa	Colon
21	chr12:40010800-40012400	Weak transcription	Left Ventricle	heart
22	chr12:40010800-40012600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:40010800-40014400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr12:40010800-40015000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:40011000-40012400	Active TSS	Fetal Brain Female	brain
26	chr12:40011400-40013800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr12:40011600-40013000	Enhancers	Primary B cells from cord blood	blood
28	chr12:40011800-40012400	Active TSS	Brain Hippocampus Middle	brain
29	chr12:40011800-40012600	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr12:40011800-40013000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:40011800-40013600	Flanking Active TSS	Primary B cells from peripheral blood	blood
32	chr12:40011800-40015200	Active TSS	Brain Cingulate Gyrus	brain
33	chr12:40012000-40012400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr12:40012000-40012400	Enhancers	Fetal Brain Male	brain
35	chr12:40012000-40012400	Enhancers	Rectal Smooth Muscle	rectum
36	chr12:40012000-40012400	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr12:40012000-40013000	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr12:40012000-40013000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chr12:40012000-40013000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:40012000-40014600	Active TSS	Brain Substantia Nigra	brain
41	chr12:40012200-40012400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:40012200-40012400	Active TSS	Brain Anterior Caudate	brain
43	chr12:40012200-40012400	Active TSS	Thymus	Thymus
44	chr12:40012200-40012600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr12:40012200-40012600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:40012200-40013200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr12:40012200-40013600	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr12:40012200-40014600	Active TSS	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links