Variant report

Variant	rs10878226
Chromosome Location	chr12:40617692-40617693
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	POLR2A	chr12:40616826-40620140	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr12:40616780-40621231	GM18951	blood:	n/a	n/a
3	POLR2A	chr12:40617283-40620948	GM18526	blood:	n/a	n/a
4	POLR2A	chr12:40616564-40621335	GM19099	blood:	n/a	n/a
5	TBP	chr12:40617611-40617941	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:40617353-40620863	GM15510	blood:	n/a	n/a
7	POLR2A	chr12:40616903-40621176	GM19193	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40615913..40618239-chr12:40619276..40621204,2	K562	blood:

Variant related genes	Relation type
LRRK2	TF binding region
ENSG00000225342	TF binding region
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10878246	1.00[YRI][hapmap]
rs11175620	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11175645	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11175655	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11175658	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11175666	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11564122	1.00[YRI][hapmap]
rs11564273	0.89[AFR][1000 genomes]
rs17442853	0.85[YRI][hapmap]
rs17458836	0.85[YRI][hapmap]
rs17458974	0.83[YRI][hapmap]
rs17519573	1.00[YRI][hapmap]
rs7294619	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7305155	0.88[YRI][hapmap]

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	nsv1052661	chr12:40603049-40642812	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40611000-40618000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:40615400-40618000	Active TSS	Primary hematopoietic stem cells	blood
3	chr12:40616000-40619200	Active TSS	Monocytes-CD14+_RO01746	blood
4	chr12:40616000-40621200	Active TSS	Primary monocytes fromperipheralblood	blood
5	chr12:40616600-40617800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr12:40616600-40619000	Active TSS	Primary B cells from peripheral blood	blood
7	chr12:40616600-40621000	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr12:40616800-40618800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:40616800-40620800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:40617000-40620600	Active TSS	Fetal Kidney	kidney
11	chr12:40617200-40617800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:40617200-40617800	Enhancers	Brain Substantia Nigra	brain
13	chr12:40617400-40617800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:40617400-40617800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:40617400-40617800	Active TSS	Primary B cells from cord blood	blood
16	chr12:40617400-40617800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:40617400-40617800	Enhancers	Muscle Satellite Cultured Cells	--
18	chr12:40617400-40617800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:40617400-40617800	Flanking Active TSS	Liver	Liver
20	chr12:40617400-40617800	Flanking Active TSS	Colon Smooth Muscle	Colon
21	chr12:40617400-40617800	Flanking Active TSS	Rectal Smooth Muscle	rectum
22	chr12:40617400-40618000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
23	chr12:40617400-40618000	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr12:40617400-40618000	Flanking Active TSS	A549	lung
25	chr12:40617400-40618000	Enhancers	HMEC	breast
26	chr12:40617400-40618200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
27	chr12:40617400-40619000	Active TSS	Duodenum Mucosa	Duodenum
28	chr12:40617400-40619200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:40617400-40619400	Active TSS	Small Intestine	intestine
30	chr12:40617400-40619600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:40617400-40619800	Active TSS	NHDF-Ad	bronchial
32	chr12:40617400-40620600	Active TSS	Stomach Smooth Muscle	stomach
33	chr12:40617400-40620800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:40617400-40620800	Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr12:40617400-40621000	Active TSS	Rectal Mucosa Donor 29	rectum
36	chr12:40617400-40621000	Active TSS	Right Atrium	heart
37	chr12:40617400-40621400	Active TSS	Aorta	Aorta
38	chr12:40617600-40617800	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:40617600-40617800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
40	chr12:40617600-40617800	Enhancers	Brain Cingulate Gyrus	brain
41	chr12:40617600-40617800	Flanking Active TSS	Brain Hippocampus Middle	brain
42	chr12:40617600-40617800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr12:40617600-40617800	Flanking Bivalent TSS/Enh	Fetal Lung	lung
44	chr12:40617600-40617800	Enhancers	Fetal Stomach	stomach
45	chr12:40617600-40618200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
46	chr12:40617600-40618200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr12:40617600-40618200	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
48	chr12:40617600-40619800	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr12:40617600-40620200	Active TSS	Ovary	ovary
50	chr12:40617600-40620200	Active TSS	Skeletal Muscle Female	skeletal muscle

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