Variant report

Variant	rs6580534
Chromosome Location	chr5:147568820-147568821
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 136 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10041939	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10043288	0.84[AMR][1000 genomes]
rs10052031	0.87[AMR][1000 genomes]
rs10055396	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10058776	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10059441	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10063951	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10067334	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10074328	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10077607	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10079388	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10079716	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10477363	0.82[EUR][1000 genomes]
rs10491344	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168037	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168038	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168039	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168041	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11743040	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11743518	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743523	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11745313	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11748034	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12188857	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12189210	0.91[EUR][1000 genomes]
rs12332436	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12332677	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12515246	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12515885	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12516461	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12519059	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12519106	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12519629	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12521387	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12522694	0.92[EUR][1000 genomes]
rs12653723	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12653724	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12717963	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13154742	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13174534	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13174816	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13174845	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13175245	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13179181	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13185600	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1368305	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1368306	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1432689	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1558410	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17096690	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17096693	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17107871	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1812484	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1897532	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1897533	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1974627	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1974628	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1974629	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2017896	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2159661	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2191681	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2400493	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2400494	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2400495	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2400496	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2400497	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2400498	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28406596	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28624399	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28667181	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28701955	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34211205	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34258096	0.86[EUR][1000 genomes]
rs34339574	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34506706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35217112	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35491588	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35507985	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35696310	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs36056267	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4133459	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4259160	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4270684	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4452547	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4498243	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4499819	0.91[EUR][1000 genomes]
rs4705230	0.80[AMR][1000 genomes]
rs4705231	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4705232	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4705233	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4705234	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6580532	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6580533	0.84[EUR][1000 genomes]
rs6580535	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6580536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6860003	0.85[EUR][1000 genomes]
rs6864124	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6865006	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6865474	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6867695	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6868569	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6869054	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6870548	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6871633	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6875563	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6884944	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6896988	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7442844	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7442875	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7444240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7445428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7445725	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7448271	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7449160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs767568	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs767569	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs767570	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7702990	0.89[EUR][1000 genomes]
rs7703690	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7703761	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7705007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7716861	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7717699	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7719535	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7732604	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9325084	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9325087	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9325088	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs963016	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9885020	0.85[EUR][1000 genomes]
rs9885270	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9885333	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9885451	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883015	chr5:147404281-147751035	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv830515	chr5:147460852-147602247	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv1843289	chr5:147554337-147576457	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6580534	SPINK6	cis	Esophagus Mucosa	GTEx
rs6580534	FBXO38	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147566600-147571200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:147567200-147571800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:147567200-147572000	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr5:147567200-147572200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:147567200-147572200	Weak transcription	Hela-S3	cervix
6	chr5:147567400-147572000	Weak transcription	Monocytes-CD14+_RO01746	blood

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