Variant report

Variant	rs10506153
Chromosome Location	chr12:40725571-40725572
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10878244	0.81[GIH][hapmap];1.00[ASN][1000 genomes]
rs10878246	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[ASN][1000 genomes]
rs11175655	0.84[GIH][hapmap]
rs11564128	0.90[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564203	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564204	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564205	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564207	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564267	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564269	1.00[CHD][hapmap]
rs11829088	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11834950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491936	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17443552	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17444096	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17444542	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17444612	1.00[ASN][1000 genomes]
rs17465912	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17466037	1.00[CHB][hapmap]
rs17466339	1.00[CHB][hapmap];0.87[AMR][1000 genomes]
rs17466430	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17467095	1.00[CHB][hapmap]
rs17491061	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17492082	1.00[ASN][1000 genomes]
rs17492138	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17519573	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17520251	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17520278	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1907632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1907633	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2114567	1.00[ASN][1000 genomes]
rs2244534	1.00[CHB][hapmap]
rs2708405	1.00[CHD][hapmap]
rs57997594	1.00[ASN][1000 genomes]
rs60776971	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61007767	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73094605	1.00[ASN][1000 genomes]
rs73100409	1.00[ASN][1000 genomes]
rs73100414	1.00[ASN][1000 genomes]
rs73110067	1.00[ASN][1000 genomes]
rs73110075	1.00[ASN][1000 genomes]
rs73275761	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73279554	1.00[ASN][1000 genomes]
rs73279557	1.00[ASN][1000 genomes]
rs9705735	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10506153	SERPINB8	trans	brain	seeQTL
rs10506153	LRRK2	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40640600-40727400	Weak transcription	Spleen	Spleen
2	chr12:40640600-40768200	Weak transcription	Pancreas	Pancrea
3	chr12:40656800-40746400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr12:40674400-40760400	Weak transcription	Lung	lung
5	chr12:40681200-40763000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:40687200-40765000	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr12:40712000-40736600	Weak transcription	Left Ventricle	heart
8	chr12:40712000-40743400	Weak transcription	Aorta	Aorta
9	chr12:40714200-40759200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr12:40716800-40761600	Weak transcription	Fetal Kidney	kidney
11	chr12:40719600-40735200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr12:40721000-40734000	Weak transcription	Esophagus	oesophagus
13	chr12:40721600-40726000	Strong transcription	Stomach Smooth Muscle	stomach
14	chr12:40722400-40725600	Strong transcription	Skeletal Muscle Female	skeletal muscle
15	chr12:40722400-40726200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:40722400-40730800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr12:40722400-40736200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:40722600-40728600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr12:40722600-40730200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:40722800-40755800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr12:40723200-40725600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:40723800-40725600	ZNF genes & repeats	A549	lung
23	chr12:40724000-40731600	Weak transcription	Brain Angular Gyrus	brain
24	chr12:40724200-40729600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:40724200-40731400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr12:40724600-40745400	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr12:40724800-40728600	Weak transcription	Colon Smooth Muscle	Colon
28	chr12:40724800-40729600	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr12:40724800-40751000	Weak transcription	Brain Anterior Caudate	brain
30	chr12:40725000-40726000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr12:40725000-40726000	Strong transcription	Ovary	ovary
32	chr12:40725000-40730000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr12:40725000-40736200	Weak transcription	Brain Hippocampus Middle	brain
34	chr12:40725000-40739200	Strong transcription	Primary B cells from peripheral blood	blood
35	chr12:40725200-40725600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:40725200-40725600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr12:40725200-40727000	Weak transcription	Adipose Nuclei	Adipose
38	chr12:40725200-40732200	Strong transcription	Liver	Liver
39	chr12:40725200-40733200	Strong transcription	Primary B cells from cord blood	blood
40	chr12:40725200-40761200	Weak transcription	Psoas Muscle	Psoas
41	chr12:40725400-40731200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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