Variant report

Variant	rs6779517
Chromosome Location	chr3:48384388-48384389
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 30 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11130165	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130166	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11706277	0.92[JPT][hapmap]
rs11706939	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11709691	0.83[JPT][hapmap]
rs11710257	0.91[JPT][hapmap]
rs11710861	0.83[JPT][hapmap];0.93[YRI][hapmap]
rs11714176	0.90[JPT][hapmap]
rs11716371	0.92[JPT][hapmap]
rs11718329	0.83[JPT][hapmap]
rs11718350	0.92[JPT][hapmap]
rs12185901	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12486935	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12486944	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12498074	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13059037	0.83[JPT][hapmap]
rs13061269	0.92[JPT][hapmap]
rs13068265	0.82[JPT][hapmap]
rs13069884	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13079728	0.92[JPT][hapmap]
rs13082217	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13082269	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082859	0.92[JPT][hapmap]
rs13084616	0.92[JPT][hapmap]
rs13085251	0.92[JPT][hapmap]
rs13087050	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13090538	0.92[JPT][hapmap]
rs13094496	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13094727	0.83[JPT][hapmap]
rs1471217	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17593974	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17647717	0.83[JPT][hapmap]
rs2017858	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2017859	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2541	0.92[JPT][hapmap]
rs3197223	0.92[JPT][hapmap]
rs34008503	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35460860	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3729577	0.83[JPT][hapmap]
rs3731513	0.83[JPT][hapmap]
rs3731534	0.82[JPT][hapmap]
rs3731555	0.83[JPT][hapmap]
rs3937	0.83[JPT][hapmap];0.94[YRI][hapmap]
rs4479622	0.92[JPT][hapmap]
rs62263035	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263037	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263038	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442111	0.83[JPT][hapmap];0.94[YRI][hapmap]
rs6791930	0.81[JPT][hapmap]
rs6794644	0.83[JPT][hapmap]
rs6800492	0.83[JPT][hapmap]
rs6801801	0.83[JPT][hapmap];0.94[YRI][hapmap]
rs6804828	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs71323399	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs745116	0.83[JPT][hapmap];0.88[YRI][hapmap]
rs7621785	0.92[JPT][hapmap]
rs9311421	0.83[JPT][hapmap]
rs936426	0.83[JPT][hapmap]
rs936427	0.83[JPT][hapmap]
rs9819094	0.83[JPT][hapmap];0.94[YRI][hapmap]
rs9825637	0.92[JPT][hapmap];0.93[YRI][hapmap]
rs9830016	0.83[JPT][hapmap];0.93[YRI][hapmap]
rs9833309	0.83[JPT][hapmap]
rs9837228	0.83[JPT][hapmap];0.94[YRI][hapmap]
rs9847953	0.83[JPT][hapmap];0.94[YRI][hapmap]
rs9850672	0.83[JPT][hapmap];0.88[YRI][hapmap]

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	nsv834683	chr3:48301504-48493261	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:30)

SNP	Gene	Cis/trans	Tissue	Source
rs6779517	ZNF589	cis	Thyroid	GTEx
rs6779517	CDC25A	cis	cerebellum	SCAN
rs6779517	MRPS18AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs6779517	NME6	cis	cerebellum	SCAN
rs6779517	MRPS18AP1	cis	Artery Aorta	GTEx
rs6779517	TMIE	cis	cerebellum	SCAN
rs6779517	ZNF589	cis	Artery Aorta	GTEx
rs6779517	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs6779517	ZNF589	cis	Esophagus Muscularis	GTEx
rs6779517	ZNF589	cis	Skin Sun Exposed Lower leg	GTEx
rs6779517	MAP4	cis	cerebellum	SCAN
rs6779517	NME6	Cis_1M	lymphoblastoid	RTeQTL
rs6779517	AMT	cis	parietal	SCAN
rs6779517	CDC25A	cis	Thyroid	GTEx
rs6779517	NME6	cis	Adipose Subcutaneous	GTEx
rs6779517	CDC25A	cis	Adipose Subcutaneous	GTEx
rs6779517	NME6	cis	Nerve Tibial	GTEx
rs6779517	MRPS18AP1	cis	Thyroid	GTEx
rs6779517	NME6	cis	Esophagus Muscularis	GTEx
rs6779517	ZNF589	cis	parietal	SCAN
rs6779517	DALRD3	cis	cerebellum	SCAN
rs6779517	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs6779517	MRPS18AP1	cis	lung	GTEx
rs6779517	MRPS18AP1	cis	Esophagus Mucosa	GTEx
rs6779517	ZNF589	cis	Brain Pons	GTEx
rs6779517	ZNF589	cis	Esophagus Mucosa	GTEx
rs6779517	CDC25A	cis	Muscle Skeletal	GTEx
rs6779517	NME6	cis	lymphoblastoid	seeQTL
rs6779517	ZNF589	cis	cerebellum	SCAN
rs6779517	MRPS18AP1	cis	Artery Tibial	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48377600-48387800	Weak transcription	Placenta	Placenta
2	chr3:48381000-48386200	Weak transcription	HSMM	muscle
3	chr3:48381200-48386000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:48384200-48385000	Enhancers	Primary neutrophils fromperipheralblood	blood

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