Variant report

Variant	rs10517283
Chromosome Location	chr4:54051213-54051214
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1038354	0.88[JPT][hapmap]
rs10517276	1.00[JPT][hapmap]
rs11133245	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12641339	1.00[JPT][hapmap]
rs13104284	1.00[JPT][hapmap]
rs13112198	0.88[JPT][hapmap]
rs13114411	1.00[JPT][hapmap]
rs13118564	1.00[JPT][hapmap]
rs13119115	1.00[JPT][hapmap]
rs13119284	1.00[JPT][hapmap]
rs13120634	0.83[JPT][hapmap]
rs13122159	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13122232	1.00[JPT][hapmap]
rs13123149	1.00[JPT][hapmap]
rs13123263	1.00[JPT][hapmap]
rs13132859	1.00[JPT][hapmap]
rs13140358	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13141532	1.00[JPT][hapmap]
rs13152478	0.88[JPT][hapmap]
rs17082362	1.00[JPT][hapmap]
rs17703292	0.81[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs17705995	1.00[YRI][hapmap]
rs28458206	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28467481	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2898961	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34421599	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4398582	1.00[JPT][hapmap]
rs4864724	1.00[JPT][hapmap]
rs6822050	0.82[JPT][hapmap]
rs71597822	0.93[ASN][1000 genomes]
rs9968315	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9998819	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[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	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10517283	PDGFRA	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54004200-54052200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:54011600-54052200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:54036600-54052200	Weak transcription	HSMM	muscle
4	chr4:54038800-54054800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:54039800-54052200	Weak transcription	HSMMtube	muscle
6	chr4:54040000-54052200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:54040000-54052200	Weak transcription	NHDF-Ad	bronchial
8	chr4:54040600-54052000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:54043200-54077000	Weak transcription	Primary T cells from cord blood	blood
10	chr4:54046400-54052400	Weak transcription	NH-A	brain
11	chr4:54048000-54086000	Weak transcription	GM12878-XiMat	blood
12	chr4:54048600-54052200	Weak transcription	Fetal Heart	heart
13	chr4:54048800-54051600	Weak transcription	Aorta	Aorta
14	chr4:54048800-54052000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:54048800-54052000	Weak transcription	Osteobl	bone
16	chr4:54049200-54051600	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr4:54049200-54052000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr4:54049800-54053600	Weak transcription	NHLF	lung
19	chr4:54050000-54053000	Strong transcription	Primary B cells from cord blood	blood
20	chr4:54050200-54052200	Weak transcription	K562	blood
21	chr4:54050200-54061800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:54050400-54062400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr4:54050600-54051600	Weak transcription	Ovary	ovary
24	chr4:54050800-54053600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:54051000-54052000	Weak transcription	Fetal Lung	lung
26	chr4:54051000-54052200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr4:54051000-54073000	Weak transcription	Primary T helper cells fromperipheralblood	blood

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