Variant report

Variant	rs12304648
Chromosome Location	chr12:40617221-40617222
allele	C/T
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	GATA3	chr12:40617193-40617393	SH-SY5Y	brain:	n/a	n/a
2	POLR2A	chr12:40616826-40620140	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr12:40616780-40621231	GM18951	blood:	n/a	n/a
4	POLR2A	chr12:40616564-40621335	GM19099	blood:	n/a	n/a
5	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
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12296317	0.97[AFR][1000 genomes]
rs12296596	0.88[AFR][1000 genomes]
rs12296964	0.88[AFR][1000 genomes]
rs12306744	0.88[AFR][1000 genomes]
rs12308447	0.86[AFR][1000 genomes]
rs12312800	0.86[AFR][1000 genomes]
rs17489951	0.94[AFR][1000 genomes]
rs17489964	0.84[AFR][1000 genomes]
rs17490300	0.97[AFR][1000 genomes]
rs7135556	1.00[AFR][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	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:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40611000-40618000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:40611200-40617400	Weak transcription	A549	lung
3	chr12:40615400-40617400	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr12:40615400-40618000	Active TSS	Primary hematopoietic stem cells	blood
5	chr12:40615600-40617400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:40616000-40619200	Active TSS	Monocytes-CD14+_RO01746	blood
7	chr12:40616000-40621200	Active TSS	Primary monocytes fromperipheralblood	blood
8	chr12:40616600-40617400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:40616600-40617400	Active TSS	Primary T cells from cord blood	blood
10	chr12:40616600-40617400	Enhancers	Adipose Nuclei	Adipose
11	chr12:40616600-40617400	Enhancers	Brain Anterior Caudate	brain
12	chr12:40616600-40617400	Enhancers	Colon Smooth Muscle	Colon
13	chr12:40616600-40617800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr12:40616600-40619000	Active TSS	Primary B cells from peripheral blood	blood
15	chr12:40616600-40621000	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr12:40616800-40617600	Bivalent/Poised TSS	GM12878-XiMat	blood
17	chr12:40616800-40618800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
18	chr12:40616800-40620800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
19	chr12:40617000-40620600	Active TSS	Fetal Kidney	kidney
20	chr12:40617200-40617400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:40617200-40617400	Enhancers	Liver	Liver
22	chr12:40617200-40617400	Enhancers	Rectal Smooth Muscle	rectum
23	chr12:40617200-40617800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:40617200-40617800	Enhancers	Brain Substantia Nigra	brain

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