Variant report

Variant	rs60538413
Chromosome Location	chr4:106952235-106952236
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 208 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:206)

rs_ID	r²[population]
rs10000428	0.88[EUR][1000 genomes]
rs10002288	0.90[ASN][1000 genomes]
rs10003024	0.88[EUR][1000 genomes]
rs10004611	0.88[EUR][1000 genomes]
rs10008428	0.88[EUR][1000 genomes]
rs10008773	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs10017969	0.87[EUR][1000 genomes]
rs10025052	0.94[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10027207	0.88[EUR][1000 genomes]
rs10030019	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10049933	0.88[EUR][1000 genomes]
rs10084928	0.89[ASN][1000 genomes]
rs10516532	0.89[ASN][1000 genomes]
rs10516533	0.84[ASN][1000 genomes]
rs11097912	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11097914	0.89[ASN][1000 genomes]
rs11097916	0.89[ASN][1000 genomes]
rs11097917	0.89[ASN][1000 genomes]
rs11097919	0.89[ASN][1000 genomes]
rs11097924	0.84[ASN][1000 genomes]
rs11097925	0.84[ASN][1000 genomes]
rs11732251	0.95[EUR][1000 genomes]
rs11732791	0.81[EUR][1000 genomes]
rs11931386	0.81[EUR][1000 genomes]
rs11932523	0.94[EUR][1000 genomes]
rs11942153	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12499891	0.89[ASN][1000 genomes]
rs12502764	0.84[ASN][1000 genomes]
rs12503753	0.86[ASN][1000 genomes]
rs12504704	0.89[ASN][1000 genomes]
rs12504721	0.84[ASN][1000 genomes]
rs12505689	0.92[ASN][1000 genomes]
rs12506062	0.89[ASN][1000 genomes]
rs12506658	0.89[ASN][1000 genomes]
rs12507429	0.90[ASN][1000 genomes]
rs12507867	0.92[ASN][1000 genomes]
rs12508432	0.84[ASN][1000 genomes]
rs12508552	0.89[ASN][1000 genomes]
rs12509366	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12509640	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12509865	0.89[ASN][1000 genomes]
rs12510058	0.84[ASN][1000 genomes]
rs12510966	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12511305	0.86[ASN][1000 genomes]
rs12512683	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12512877	0.83[ASN][1000 genomes]
rs12512903	0.83[ASN][1000 genomes]
rs12512966	0.89[ASN][1000 genomes]
rs12513317	0.89[ASN][1000 genomes]
rs12639678	0.92[ASN][1000 genomes]
rs12639869	0.84[ASN][1000 genomes]
rs12641015	0.84[ASN][1000 genomes]
rs12641037	0.83[ASN][1000 genomes]
rs12642059	0.84[ASN][1000 genomes]
rs12642227	0.89[ASN][1000 genomes]
rs12642691	0.84[EUR][1000 genomes]
rs12642900	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12643397	0.89[ASN][1000 genomes]
rs12644259	0.84[ASN][1000 genomes]
rs12645271	0.89[ASN][1000 genomes]
rs12645698	0.80[ASN][1000 genomes]
rs12646263	0.86[ASN][1000 genomes]
rs12646485	0.89[ASN][1000 genomes]
rs12647078	0.89[ASN][1000 genomes]
rs12649709	0.84[ASN][1000 genomes]
rs12651360	0.84[ASN][1000 genomes]
rs13101612	0.84[EUR][1000 genomes]
rs13113845	0.81[EUR][1000 genomes]
rs13114479	0.81[EUR][1000 genomes]
rs13121614	0.81[EUR][1000 genomes]
rs13138528	0.81[EUR][1000 genomes]
rs17036613	0.84[ASN][1000 genomes]
rs17259572	0.90[ASN][1000 genomes]
rs17273093	0.89[ASN][1000 genomes]
rs17273445	0.89[ASN][1000 genomes]
rs17274017	0.84[ASN][1000 genomes]
rs17333287	0.84[ASN][1000 genomes]
rs2290607	0.89[ASN][1000 genomes]
rs28391259	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28394440	0.94[EUR][1000 genomes]
rs28467469	0.92[EUR][1000 genomes]
rs28507027	0.89[ASN][1000 genomes]
rs28765420	0.87[ASN][1000 genomes]
rs28784652	0.92[EUR][1000 genomes]
rs28787305	0.89[ASN][1000 genomes]
rs28814088	0.88[ASN][1000 genomes]
rs28822186	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28845843	0.95[EUR][1000 genomes]
rs28866820	0.89[ASN][1000 genomes]
rs28868894	0.89[ASN][1000 genomes]
rs28875879	0.89[ASN][1000 genomes]
rs28897193	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34193646	0.84[ASN][1000 genomes]
rs34961213	0.84[ASN][1000 genomes]
rs35518913	0.89[ASN][1000 genomes]
rs3775090	0.84[ASN][1000 genomes]
rs4306956	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4307042	0.87[EUR][1000 genomes]
rs4314353	0.92[EUR][1000 genomes]
rs4323181	0.89[ASN][1000 genomes]
rs4337798	0.89[ASN][1000 genomes]
rs4337799	0.89[ASN][1000 genomes]
rs4339284	0.89[ASN][1000 genomes]
rs4355394	0.94[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4364267	0.94[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4374692	0.81[EUR][1000 genomes]
rs4382109	0.87[EUR][1000 genomes]
rs4422480	0.89[ASN][1000 genomes]
rs4429790	0.89[ASN][1000 genomes]
rs4458525	0.89[ASN][1000 genomes]
rs4466113	0.89[ASN][1000 genomes]
rs4470632	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4508971	0.92[EUR][1000 genomes]
rs4521418	0.88[ASN][1000 genomes]
rs4569824	0.81[EUR][1000 genomes]
rs4577583	0.94[EUR][1000 genomes]
rs4600995	0.87[EUR][1000 genomes]
rs55633564	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55634475	0.89[ASN][1000 genomes]
rs55833794	0.89[ASN][1000 genomes]
rs56009469	0.84[ASN][1000 genomes]
rs56135499	0.89[ASN][1000 genomes]
rs56222430	0.80[ASN][1000 genomes]
rs56231393	0.84[ASN][1000 genomes]
rs56260521	0.89[ASN][1000 genomes]
rs56329826	0.89[ASN][1000 genomes]
rs56333662	0.84[ASN][1000 genomes]
rs56341229	0.89[ASN][1000 genomes]
rs56775039	0.84[ASN][1000 genomes]
rs57246774	0.89[ASN][1000 genomes]
rs59784613	0.89[ASN][1000 genomes]
rs61544154	0.84[ASN][1000 genomes]
rs62321365	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6533237	0.95[EUR][1000 genomes]
rs6533240	0.89[ASN][1000 genomes]
rs6533242	0.81[EUR][1000 genomes]
rs6533243	0.84[ASN][1000 genomes]
rs6810877	0.87[ASN][1000 genomes]
rs6815014	0.89[ASN][1000 genomes]
rs6816614	0.89[ASN][1000 genomes]
rs6818197	0.89[ASN][1000 genomes]
rs6818626	0.89[ASN][1000 genomes]
rs6819081	0.84[EUR][1000 genomes]
rs6822692	0.89[ASN][1000 genomes]
rs6823347	0.94[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6824682	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6828362	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6829795	0.89[ASN][1000 genomes]
rs6835216	0.89[ASN][1000 genomes]
rs6836198	0.87[EUR][1000 genomes]
rs6842919	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6843331	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6843870	0.89[ASN][1000 genomes]
rs6844324	0.89[ASN][1000 genomes]
rs6846579	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6852388	0.96[EUR][1000 genomes]
rs72489522	0.89[ASN][1000 genomes]
rs72677306	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72893620	0.84[ASN][1000 genomes]
rs7340989	0.82[ASN][1000 genomes]
rs7438546	0.95[EUR][1000 genomes]
rs7655054	0.89[ASN][1000 genomes]
rs7657962	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7657975	0.89[ASN][1000 genomes]
rs7658011	0.90[ASN][1000 genomes]
rs7658701	0.89[ASN][1000 genomes]
rs7661499	0.84[ASN][1000 genomes]
rs7661565	0.89[ASN][1000 genomes]
rs7662219	0.84[ASN][1000 genomes]
rs7662291	0.84[ASN][1000 genomes]
rs7662395	0.84[ASN][1000 genomes]
rs7662592	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7662806	0.89[ASN][1000 genomes]
rs7662836	0.89[ASN][1000 genomes]
rs7664032	0.89[ASN][1000 genomes]
rs7664188	0.89[ASN][1000 genomes]
rs7665946	0.84[ASN][1000 genomes]
rs7667719	0.84[ASN][1000 genomes]
rs7668276	0.81[EUR][1000 genomes]
rs7668477	0.84[ASN][1000 genomes]
rs7669087	0.89[ASN][1000 genomes]
rs7669212	0.84[ASN][1000 genomes]
rs7671145	0.87[ASN][1000 genomes]
rs7673101	0.88[EUR][1000 genomes]
rs7674381	0.83[ASN][1000 genomes]
rs7674466	0.83[ASN][1000 genomes]
rs7674931	0.84[ASN][1000 genomes]
rs7675728	0.92[ASN][1000 genomes]
rs7677248	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7678229	0.89[ASN][1000 genomes]
rs7678847	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7681257	0.89[ASN][1000 genomes]
rs7682646	0.85[EUR][1000 genomes]
rs7687657	0.91[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7688411	0.84[ASN][1000 genomes]
rs7689298	0.95[EUR][1000 genomes]
rs7692069	0.94[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7693333	0.87[EUR][1000 genomes]
rs7693448	0.81[EUR][1000 genomes]
rs7698386	0.88[ASN][1000 genomes]
rs7699768	0.89[ASN][1000 genomes]
rs9684658	0.84[ASN][1000 genomes]
rs9685018	0.87[ASN][1000 genomes]
rs9685464	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9991091	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9996093	0.88[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	nsv1014993	chr4:106796019-106980727	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv522792	chr4:106895964-106982793	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs60538413	MGC16169	Cis_1M	lymphoblastoid	RTeQTL
rs60538413	SCYE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106950600-106954000	Weak transcription	Pancreas	Pancrea
2	chr4:106951200-106953800	Weak transcription	HepG2	liver
3	chr4:106951800-106954000	Weak transcription	Esophagus	oesophagus

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