Variant report

Variant	rs9489173
Chromosome Location	chr6:117755267-117755268
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs13192511	0.89[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs13195478	0.83[JPT][hapmap]
rs13195673	0.89[JPT][hapmap]
rs13205986	0.84[JPT][hapmap]
rs13207962	0.84[JPT][hapmap]
rs13208369	0.88[ASN][1000 genomes]
rs13210963	0.82[JPT][hapmap]
rs13211956	0.86[JPT][hapmap]
rs13212002	0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs13218378	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs1407181	0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1407182	0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs17079188	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17079281	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs1853146	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1853147	0.90[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1885064	0.83[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2104064	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs2243	0.91[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs2273601	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.80[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs34925922	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs3777980	1.00[JPT][hapmap]
rs3777982	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6910338	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6930292	0.94[ASW][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.93[LWK][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6936540	0.83[ASN][1000 genomes]
rs6941824	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6942067	0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs717969	0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs717970	0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs722359	0.84[JPT][hapmap]
rs7739294	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7746536	0.84[JPT][hapmap]
rs7749229	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7756187	0.82[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs7763979	0.84[JPT][hapmap]
rs9374658	0.91[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs9481719	0.89[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs9489152	0.90[JPT][hapmap]
rs9489155	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9489157	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9489158	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9489166	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9489193	1.00[ASW][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9489199	0.92[CHB][hapmap];0.94[JPT][hapmap];0.91[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9489173	C6orf204	cis	cerebellum	SCAN
rs9489173	GOPC	cis	cerebellum	SCAN
rs9489173	DCBLD1	cis	multi-tissue	Pritchard

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:117747600-117760600	Weak transcription	Osteobl	bone
2	chr6:117753200-117760200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr6:117753800-117757000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:117753800-117760000	Weak transcription	HSMM	muscle
5	chr6:117753800-117760400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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