Variant report

Variant	rs552183
Chromosome Location	chr6:117631431-117631432
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs17079053	0.89[EUR][1000 genomes]
rs17632578	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1894674	1.00[CEU][hapmap];0.94[CHD][hapmap];0.85[MEX][hapmap];0.89[EUR][1000 genomes]
rs2243385	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2243386	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2301485	1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[MEX][hapmap];0.89[EUR][1000 genomes]
rs2301486	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs3756891	1.00[CEU][hapmap];0.89[CHD][hapmap];0.85[MEX][hapmap];0.87[EUR][1000 genomes]
rs473006	0.89[EUR][1000 genomes]
rs489576	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs492132	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs493451	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs493548	0.89[EUR][1000 genomes]
rs497186	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[MEX][hapmap];0.89[EUR][1000 genomes]
rs498251	0.89[EUR][1000 genomes]
rs499199	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs499338	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs499599	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs501109	0.93[CEU][hapmap];0.84[CHD][hapmap];0.89[EUR][1000 genomes]
rs506557	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs508278	0.82[CEU][hapmap]
rs518987	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs528633	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[MEX][hapmap];0.89[EUR][1000 genomes]
rs530066	0.82[CEU][hapmap];0.85[MEX][hapmap];0.80[EUR][1000 genomes]
rs530713	0.89[EUR][1000 genomes]
rs541866	0.88[EUR][1000 genomes]
rs543230	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs543706	0.89[EUR][1000 genomes]
rs545537	0.89[EUR][1000 genomes]
rs546631	0.80[EUR][1000 genomes]
rs549557	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs568514	0.89[EUR][1000 genomes]
rs573886	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs574664	0.89[EUR][1000 genomes]
rs575006	0.89[EUR][1000 genomes]
rs580099	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs581235	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs584647	0.80[EUR][1000 genomes]
rs592757	0.89[EUR][1000 genomes]
rs61077141	0.85[EUR][1000 genomes]
rs680920	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs687218	0.89[EUR][1000 genomes]
rs73566821	0.86[EUR][1000 genomes]
rs9481702	0.80[EUR][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	nsv948766	chr6:117407275-117641016	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv532050	chr6:117528154-118203005	ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs552183	PAOX	trans	parietal	SCAN
rs552183	MFSD3	trans	parietal	SCAN
rs552183	FAM26D	cis	parietal	SCAN
rs552183	GOPC	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:117625800-117646600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:117627800-117635000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:117628000-117643800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:117630600-117633200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:117631400-117643400	Weak transcription	HSMMtube	muscle
6	chr6:117631400-117649200	Weak transcription	HSMM	muscle

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