Variant report

Variant	rs2020059
Chromosome Location	chr4:171418411-171418412
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:171180855..171182050-chr4:171418061..171418844,5	MCF-7	breast:

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs13120637	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2135900	0.85[EUR][1000 genomes]
rs2612401	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2661081	0.82[ASN][1000 genomes]
rs906445	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv432673	chr4:171340897-171423121	Active TSS Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv880492	chr4:171386268-171433137	Active TSS Flanking Active TSS Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1032666	chr4:171402225-171552857	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2020059	PALLD	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:171418000-171418800	Active TSS	Dnd41	blood
2	chr4:171418000-171419000	Active TSS	GM12878-XiMat	blood
3	chr4:171418000-171419800	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr4:171418200-171418600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:171418200-171418600	Active TSS	Right Atrium	heart
6	chr4:171418200-171418600	Active TSS	NH-A	brain
7	chr4:171418200-171418800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr4:171418200-171418800	Active TSS	Brain Angular Gyrus	brain
9	chr4:171418200-171418800	Active TSS	Brain Cingulate Gyrus	brain
10	chr4:171418200-171418800	Active TSS	Brain Hippocampus Middle	brain
11	chr4:171418200-171418800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:171418200-171418800	Active TSS	Duodenum Mucosa	Duodenum
13	chr4:171418200-171418800	Active TSS	Fetal Kidney	kidney
14	chr4:171418200-171418800	Active TSS	Ovary	ovary
15	chr4:171418200-171418800	Active TSS	Thymus	Thymus
16	chr4:171418200-171418800	Active TSS	Hela-S3	cervix
17	chr4:171418200-171418800	Active TSS	HepG2	liver
18	chr4:171418200-171419000	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr4:171418200-171419000	Active TSS	Primary B cells from cord blood	blood
20	chr4:171418200-171419000	Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr4:171418200-171419000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:171418200-171419000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:171418200-171419000	Active TSS	Aorta	Aorta
24	chr4:171418200-171419000	Active TSS	Brain Anterior Caudate	brain
25	chr4:171418200-171419000	Active TSS	HMEC	breast
26	chr4:171418200-171419000	Active TSS	Monocytes-CD14+_RO01746	blood
27	chr4:171418200-171419200	Active TSS	Primary hematopoietic stem cells	blood
28	chr4:171418200-171419200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr4:171418200-171419200	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr4:171418400-171418800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:171418400-171418800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:171418400-171418800	Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr4:171418400-171418800	Flanking Active TSS	Brain Germinal Matrix	brain
34	chr4:171418400-171418800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr4:171418400-171418800	Active TSS	A549	lung
36	chr4:171418400-171418800	Active TSS	Osteobl	bone

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