Variant report

Variant	rs17442733
Chromosome Location	chr9:72590091-72590092
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10217790	0.92[ASN][1000 genomes]
rs1027282	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10511978	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10868348	0.99[ASN][1000 genomes]
rs11141101	0.99[ASN][1000 genomes]
rs11141106	0.97[ASN][1000 genomes]
rs11141122	0.97[ASN][1000 genomes]
rs11141127	0.80[ASN][1000 genomes]
rs11141246	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11141260	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11788010	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11789512	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11790329	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12336812	0.97[ASN][1000 genomes]
rs12353051	0.97[ASN][1000 genomes]
rs12353052	0.97[ASN][1000 genomes]
rs12551035	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12551904	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12552060	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12554412	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12554849	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12555905	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12683555	0.97[ASN][1000 genomes]
rs12683959	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12686422	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12686803	0.97[ASN][1000 genomes]
rs17443354	0.97[ASN][1000 genomes]
rs17522643	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17522671	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2131427	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2131428	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2172432	0.97[ASN][1000 genomes]
rs2201232	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2220736	0.96[ASN][1000 genomes]
rs2220737	0.97[ASN][1000 genomes]
rs4256644	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56380265	0.97[ASN][1000 genomes]
rs56399669	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57388366	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61210535	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62572583	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62572585	0.97[ASN][1000 genomes]
rs62572586	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62572589	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62572598	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62572600	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62572601	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62572604	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62572605	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs66542913	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7026012	0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7026154	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73456376	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893438	chr9:72363992-72720438	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv831612	chr9:72473778-72634253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1049457	chr9:72539144-72765913	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1035668	chr9:72555053-72632796	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1051004	chr9:72557761-72632015	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv831613	chr9:72586058-72740061	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17442733	PTAR1	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72580400-72590600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr9:72580600-72591000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr9:72584200-72591000	Weak transcription	Esophagus	oesophagus
4	chr9:72585800-72590400	Weak transcription	HUVEC	blood vessel
5	chr9:72585800-72590800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:72587000-72590600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr9:72587000-72590600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr9:72587000-72596800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr9:72587200-72590400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr9:72587200-72590400	Weak transcription	NHLF	lung
11	chr9:72587200-72590600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr9:72587200-72590600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr9:72587200-72590600	Weak transcription	Fetal Muscle Leg	muscle
14	chr9:72587200-72590800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:72587200-72590800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr9:72587200-72590800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr9:72587400-72590600	Weak transcription	HMEC	breast
18	chr9:72587400-72590600	Weak transcription	NHDF-Ad	bronchial
19	chr9:72587400-72590600	Weak transcription	NHEK	skin
20	chr9:72587400-72590600	Weak transcription	Osteobl	bone
21	chr9:72587400-72590800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr9:72587400-72591000	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:72587800-72590600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr9:72588200-72590200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr9:72589000-72590800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr9:72589200-72591200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr9:72589400-72590800	Enhancers	HSMM	muscle
28	chr9:72589400-72590800	Enhancers	HSMMtube	muscle
29	chr9:72589600-72591200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr9:72589800-72592200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr9:72589800-72592200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr9:72590000-72590800	Enhancers	Muscle Satellite Cultured Cells	--
33	chr9:72590000-72591200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr9:72590000-72592400	Enhancers	NH-A	brain

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