Variant report

Variant	rs10021772
Chromosome Location	chr4:54373464-54373465
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 4 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs4501281	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864766	0.88[LWK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs6834288	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829936	chr4:54367783-54556123	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10021772	PDGFRA	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54329600-54373600	Weak transcription	Brain Germinal Matrix	brain
2	chr4:54329800-54374000	Weak transcription	Left Ventricle	heart
3	chr4:54333000-54374800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:54343000-54385600	Weak transcription	Fetal Brain Female	brain
5	chr4:54343200-54376800	Weak transcription	Brain Anterior Caudate	brain
6	chr4:54346400-54374000	Weak transcription	Right Ventricle	heart
7	chr4:54347600-54401800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr4:54355200-54378600	Weak transcription	Fetal Brain Male	brain
9	chr4:54362400-54374200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr4:54362800-54376000	Weak transcription	Brain Angular Gyrus	brain
11	chr4:54363200-54384200	Weak transcription	Esophagus	oesophagus
12	chr4:54363800-54384000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:54365400-54374200	Weak transcription	Fetal Stomach	stomach
14	chr4:54365600-54374000	Weak transcription	Aorta	Aorta
15	chr4:54365800-54374000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr4:54366600-54373800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr4:54366600-54384200	Weak transcription	Pancreas	Pancrea
18	chr4:54368000-54376600	Weak transcription	Ovary	ovary
19	chr4:54370800-54374800	Strong transcription	Placenta	Placenta
20	chr4:54371800-54374400	Strong transcription	Fetal Intestine Large	intestine
21	chr4:54372600-54374000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr4:54372600-54375000	Strong transcription	Fetal Intestine Small	intestine
23	chr4:54372800-54388400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr4:54373200-54373600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:54373200-54373600	Enhancers	Adipose Nuclei	Adipose
26	chr4:54373200-54373800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr4:54373200-54373800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:54373200-54374400	Active TSS	Liver	Liver
29	chr4:54373200-54375600	Enhancers	NHDF-Ad	bronchial
30	chr4:54373200-54375800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr4:54373400-54373600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr4:54373400-54373600	Enhancers	NH-A	brain
33	chr4:54373400-54373800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:54373400-54373800	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr4:54373400-54373800	Flanking Active TSS	HSMMtube	muscle
36	chr4:54373400-54373800	Flanking Active TSS	Osteobl	bone
37	chr4:54373400-54374000	Enhancers	Fetal Muscle Leg	muscle
38	chr4:54373400-54374000	Enhancers	NHLF	lung
39	chr4:54373400-54374200	Enhancers	Gastric	stomach
40	chr4:54373400-54374600	Flanking Active TSS	HSMM	muscle
41	chr4:54373400-54375000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr4:54373400-54375000	Enhancers	Psoas Muscle	Psoas
43	chr4:54373400-54375000	Enhancers	Right Atrium	heart
44	chr4:54373400-54375400	Enhancers	Stomach Mucosa	stomach

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