Variant report

Variant	rs244481
Chromosome Location	chr5:52040289-52040290
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10512992	1.00[YRI][hapmap]
rs12332623	0.88[ASN][1000 genomes]
rs1303763	0.83[MEX][hapmap]
rs1626287	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1645393	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1645394	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs164611	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs164612	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1668506	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs244491	0.94[ASN][1000 genomes]
rs244493	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs244495	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs29976	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs29977	1.00[ASN][1000 genomes]
rs29980	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs29982	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs351933	0.91[ASN][1000 genomes]
rs351937	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs351940	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs39811	0.86[ASN][1000 genomes]
rs599698	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs651393	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs657796	0.90[ASN][1000 genomes]
rs658771	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs664248	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754787	chr5:51688543-52193243	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv1027410	chr5:52022713-52103360	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs244481	PPAP2A	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52037000-52041600	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr5:52037000-52042000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr5:52037200-52041600	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr5:52037200-52041600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr5:52037200-52042000	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr5:52037400-52041000	Enhancers	Dnd41	blood
7	chr5:52037400-52042200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr5:52037600-52041000	Enhancers	HUVEC	blood vessel
9	chr5:52037600-52041200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr5:52037600-52042600	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr5:52037800-52042200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr5:52038000-52041000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:52038200-52042000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr5:52038200-52042200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr5:52038400-52040400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:52038400-52042000	Weak transcription	Hela-S3	cervix
17	chr5:52038800-52040400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr5:52039000-52040400	Enhancers	NHDF-Ad	bronchial
19	chr5:52039000-52041600	Enhancers	Primary T cells fromperipheralblood	blood
20	chr5:52039200-52040800	Enhancers	Adipose Nuclei	Adipose
21	chr5:52039200-52040800	Enhancers	Left Ventricle	heart
22	chr5:52039200-52041000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:52039200-52041000	Enhancers	Duodenum Mucosa	Duodenum
24	chr5:52039200-52041400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr5:52039600-52040400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:52039600-52040600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:52039800-52040400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr5:52039800-52040800	Weak transcription	Fetal Thymus	thymus
29	chr5:52039800-52040800	Weak transcription	Stomach Mucosa	stomach
30	chr5:52040000-52040400	Enhancers	Primary hematopoietic stem cells	blood
31	chr5:52040000-52040600	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr5:52040000-52042000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr5:52040200-52040600	Weak transcription	Fetal Stomach	stomach
34	chr5:52040200-52040800	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr5:52040200-52042000	Weak transcription	Fetal Lung	lung
36	chr5:52040200-52042400	Weak transcription	Osteobl	bone
37	chr5:52040200-52043000	Enhancers	Primary T cells from cord blood	blood

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