Variant report

Variant	rs7619865
Chromosome Location	chr3:48370580-48370581
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr3:48370541-48370777	T-47D	breast:	n/a	n/a

Variant related genes	Relation type
SPINK8	TF binding region

Extended variants
information (count: 89 )
Associated
traits (count: 48 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1045482	0.94[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11130162	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11130163	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11130164	0.84[EUR][1000 genomes]
rs1134867	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11706221	0.84[EUR][1000 genomes]
rs11706277	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs11707997	0.84[EUR][1000 genomes]
rs11710257	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs11713476	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11714176	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs11714944	0.83[EUR][1000 genomes]
rs11715776	0.82[EUR][1000 genomes]
rs11716371	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs11716848	0.84[EUR][1000 genomes]
rs11717716	0.84[EUR][1000 genomes]
rs11718350	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs13060020	0.84[EUR][1000 genomes]
rs13061269	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs13066044	0.84[EUR][1000 genomes]
rs13066758	0.82[EUR][1000 genomes]
rs13067450	0.82[EUR][1000 genomes]
rs13069029	0.83[EUR][1000 genomes]
rs13070210	0.81[EUR][1000 genomes]
rs13071960	0.84[EUR][1000 genomes]
rs13079728	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs13081169	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs13081633	0.83[EUR][1000 genomes]
rs13082158	0.83[EUR][1000 genomes]
rs13082859	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs13084616	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs13085251	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs13090538	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs13095983	0.83[EUR][1000 genomes]
rs13099560	0.96[YRI][hapmap]
rs2541	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs3197223	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs34076262	0.84[EUR][1000 genomes]
rs34523942	0.82[EUR][1000 genomes]
rs34589064	0.82[EUR][1000 genomes]
rs34630841	0.82[EUR][1000 genomes]
rs34749846	0.82[EUR][1000 genomes]
rs34946886	0.82[EUR][1000 genomes]
rs35190747	0.82[EUR][1000 genomes]
rs35297395	0.82[EUR][1000 genomes]
rs35297486	0.81[EUR][1000 genomes]
rs35411187	0.83[EUR][1000 genomes]
rs35778847	0.82[EUR][1000 genomes]
rs35802497	0.82[EUR][1000 genomes]
rs35944878	0.81[EUR][1000 genomes]
rs36075665	0.82[EUR][1000 genomes]
rs36121690	0.82[EUR][1000 genomes]
rs4130522	0.83[EUR][1000 genomes]
rs4130995	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4371540	0.83[EUR][1000 genomes]
rs4392440	0.82[EUR][1000 genomes]
rs4420898	0.84[EUR][1000 genomes]
rs4479622	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs4511915	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs4511916	0.83[EUR][1000 genomes]
rs4541431	0.84[EUR][1000 genomes]
rs4619808	0.84[EUR][1000 genomes]
rs4632568	0.84[EUR][1000 genomes]
rs6442110	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6782166	0.83[EUR][1000 genomes]
rs6787500	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6791930	0.86[CEU][hapmap]
rs6793150	0.83[EUR][1000 genomes]
rs6793223	0.84[EUR][1000 genomes]
rs6793239	0.83[EUR][1000 genomes]
rs6796490	0.94[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap]
rs6804986	0.84[EUR][1000 genomes]
rs6806112	0.92[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71323394	0.83[EUR][1000 genomes]
rs71323395	0.84[EUR][1000 genomes]
rs71323396	0.83[EUR][1000 genomes]
rs71323397	0.84[EUR][1000 genomes]
rs7374376	0.93[YRI][hapmap]
rs745116	0.83[CEU][hapmap]
rs7621785	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs7624450	0.83[EUR][1000 genomes]
rs7632297	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs7645425	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs7652233	0.84[EUR][1000 genomes]
rs7653152	0.85[EUR][1000 genomes]
rs7653336	0.84[EUR][1000 genomes]
rs9825637	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs9846818	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	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:48)

SNP	Gene	Cis/trans	Tissue	Source
rs7619865	NME6	cis	multi-tissue	Pritchard
rs7619865	NME6	cis	Artery Tibial	GTEx
rs7619865	MRPS18AP1	cis	Artery Aorta	GTEx
rs7619865	ARIH2	cis	parietal	SCAN
rs7619865	MRPS18AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs7619865	ZNF589	cis	lung	GTEx
rs7619865	ZNF589	cis	parietal	SCAN
rs7619865	ZNF589	cis	Artery Tibial	GTEx
rs7619865	CDC25A	cis	Artery Tibial	GTEx
rs7619865	NME6	Cis_1M	lymphoblastoid	RTeQTL
rs7619865	ALS2CL	cis	parietal	SCAN
rs7619865	ZNF589	Cis_1M	lymphoblastoid	RTeQTL
rs7619865	NME6	cis	lymphoblastoid	seeQTL
rs7619865	CDC25A	cis	cerebellum	SCAN
rs7619865	RBM5	cis	cerebellum	SCAN
rs7619865	MRPS18AP1	cis	Heart Left Ventricle	GTEx
rs7619865	CDC25A	cis	Adipose Subcutaneous	GTEx
rs7619865	MRPS18AP1	cis	lung	GTEx
rs7619865	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs7619865	CDC25A	cis	Muscle Skeletal	GTEx
rs7619865	ZNF589	cis	Artery Aorta	GTEx
rs7619865	MRPS18AP1	cis	Nerve Tibial	GTEx
rs7619865	NME6	cis	Skin Sun Exposed Lower leg	GTEx
rs7619865	MRPS18AP1	cis	Thyroid	GTEx
rs7619865	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs7619865	ZNF589	cis	Frontal Cortex	GTEx
rs7619865	CDC25A	cis	Thyroid	GTEx
rs7619865	NME6	cis	Artery Aorta	GTEx
rs7619865	ZNF589	cis	Esophagus Mucosa	GTEx
rs7619865	ZNF589	cis	Thyroid	GTEx
rs7619865	ZNF589	cis	cerebellum	SCAN
rs7619865	ZNF589	cis	Temporal Cortex	GTEx
rs7619865	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs7619865	MRPS18AP1	cis	Whole Blood	GTEx
rs7619865	ZNF589	cis	Nerve Tibial	GTEx
rs7619865	ZNF589	cis	Whole Blood	GTEx
rs7619865	ZNF589	cis	Stomach	GTEx
rs7619865	ZNF589	cis	Brain Pons	GTEx
rs7619865	MRPS18AP1	cis	Adipose Subcutaneous	GTEx
rs7619865	MRPS18AP1	cis	Esophagus Mucosa	GTEx
rs7619865	ZNF589	cis	Cerebellum	GTEx
rs7619865	MRPS18AP1	cis	Stomach	GTEx
rs7619865	NME6	cis	cerebellum	SCAN
rs7619865	MRPS18AP1	cis	Artery Tibial	GTEx
rs7619865	NME6	cis	Nerve Tibial	GTEx
rs7619865	ZNF589	cis	Skin Sun Exposed Lower leg	GTEx
rs7619865	NME6	cis	Esophagus Muscularis	GTEx
rs7619865	ZNF589	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48363000-48373400	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr3:48370200-48370800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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