Variant report

Variant	rs12639678
Chromosome Location	chr4:106952765-106952766
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:106952681..106954677-chr4:106971571..106974056,2	K562	blood:

Extended variants
information (count: 171 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:169)

rs_ID	r²[population]
rs10002288	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10018910	0.92[EUR][1000 genomes]
rs10025052	0.97[ASN][1000 genomes]
rs10030019	0.96[ASN][1000 genomes]
rs10084928	0.96[ASN][1000 genomes]
rs10516532	0.96[ASN][1000 genomes]
rs10516533	0.91[ASN][1000 genomes]
rs11097912	0.96[ASN][1000 genomes]
rs11097914	0.96[ASN][1000 genomes]
rs11097916	0.96[ASN][1000 genomes]
rs11097917	0.96[ASN][1000 genomes]
rs11097919	0.96[ASN][1000 genomes]
rs11097924	0.91[ASN][1000 genomes]
rs11097925	0.91[ASN][1000 genomes]
rs11725254	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11942153	0.97[ASN][1000 genomes]
rs12499891	0.96[ASN][1000 genomes]
rs12502764	0.91[ASN][1000 genomes]
rs12503753	0.94[ASN][1000 genomes]
rs12504704	0.96[ASN][1000 genomes]
rs12504721	0.91[ASN][1000 genomes]
rs12505689	1.00[ASN][1000 genomes]
rs12506062	0.96[ASN][1000 genomes]
rs12506658	0.96[ASN][1000 genomes]
rs12507429	0.95[ASN][1000 genomes]
rs12507867	1.00[ASN][1000 genomes]
rs12507874	0.86[ASN][1000 genomes]
rs12508432	0.91[ASN][1000 genomes]
rs12508552	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12509366	0.96[ASN][1000 genomes]
rs12509640	0.87[ASN][1000 genomes]
rs12509865	0.96[ASN][1000 genomes]
rs12510058	0.91[ASN][1000 genomes]
rs12510966	0.96[ASN][1000 genomes]
rs12511305	0.93[ASN][1000 genomes]
rs12512683	0.96[ASN][1000 genomes]
rs12512877	0.90[ASN][1000 genomes]
rs12512903	0.90[ASN][1000 genomes]
rs12512966	0.96[ASN][1000 genomes]
rs12513317	0.96[ASN][1000 genomes]
rs12513345	0.93[EUR][1000 genomes]
rs12639869	0.91[ASN][1000 genomes]
rs12641015	0.91[ASN][1000 genomes]
rs12641037	0.90[ASN][1000 genomes]
rs12642059	0.91[ASN][1000 genomes]
rs12642227	0.96[ASN][1000 genomes]
rs12642900	0.96[ASN][1000 genomes]
rs12643397	0.96[ASN][1000 genomes]
rs12644259	0.91[ASN][1000 genomes]
rs12645271	0.96[ASN][1000 genomes]
rs12645698	0.87[ASN][1000 genomes]
rs12645743	0.86[ASN][1000 genomes]
rs12646263	0.94[ASN][1000 genomes]
rs12646485	0.96[ASN][1000 genomes]
rs12647078	0.96[ASN][1000 genomes]
rs12649709	0.91[ASN][1000 genomes]
rs12651360	0.91[ASN][1000 genomes]
rs17036613	0.91[ASN][1000 genomes]
rs17259572	0.97[ASN][1000 genomes]
rs17272618	0.92[EUR][1000 genomes]
rs17273093	0.96[ASN][1000 genomes]
rs17273445	0.96[ASN][1000 genomes]
rs17274017	0.91[ASN][1000 genomes]
rs17333287	0.91[ASN][1000 genomes]
rs2290607	0.96[ASN][1000 genomes]
rs28391259	0.96[ASN][1000 genomes]
rs28507027	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28765420	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28787305	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28805707	0.92[EUR][1000 genomes]
rs28814088	0.90[ASN][1000 genomes]
rs28822186	0.96[ASN][1000 genomes]
rs28866820	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28868894	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28875879	0.96[ASN][1000 genomes]
rs28897193	0.96[ASN][1000 genomes]
rs34193646	0.91[ASN][1000 genomes]
rs34961213	0.91[ASN][1000 genomes]
rs35518913	0.96[ASN][1000 genomes]
rs3775090	0.91[ASN][1000 genomes]
rs4306956	0.81[ASN][1000 genomes]
rs4323181	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4337798	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4337799	0.96[ASN][1000 genomes]
rs4339284	0.96[ASN][1000 genomes]
rs4422480	0.96[ASN][1000 genomes]
rs4429790	0.96[ASN][1000 genomes]
rs4458525	0.96[ASN][1000 genomes]
rs4466113	0.96[ASN][1000 genomes]
rs4521418	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55633564	0.96[ASN][1000 genomes]
rs55634475	0.96[ASN][1000 genomes]
rs55833794	0.96[ASN][1000 genomes]
rs56009469	0.91[ASN][1000 genomes]
rs56135499	0.96[ASN][1000 genomes]
rs56222430	0.87[ASN][1000 genomes]
rs56231393	0.91[ASN][1000 genomes]
rs56260521	0.96[ASN][1000 genomes]
rs56329826	0.96[ASN][1000 genomes]
rs56333662	0.91[ASN][1000 genomes]
rs56341229	0.96[ASN][1000 genomes]
rs56775039	0.91[ASN][1000 genomes]
rs57246774	0.96[ASN][1000 genomes]
rs59784613	0.96[ASN][1000 genomes]
rs60538413	0.92[ASN][1000 genomes]
rs61544154	0.91[ASN][1000 genomes]
rs62321365	0.94[ASN][1000 genomes]
rs6533240	0.96[ASN][1000 genomes]
rs6533243	0.91[ASN][1000 genomes]
rs6810877	0.94[ASN][1000 genomes]
rs6815014	0.96[ASN][1000 genomes]
rs6816614	0.96[ASN][1000 genomes]
rs6818197	0.96[ASN][1000 genomes]
rs6818626	0.96[ASN][1000 genomes]
rs6822692	0.96[ASN][1000 genomes]
rs6823347	0.97[ASN][1000 genomes]
rs6824682	0.96[ASN][1000 genomes]
rs6828362	0.96[ASN][1000 genomes]
rs6829795	0.96[ASN][1000 genomes]
rs6835216	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6842919	0.99[ASN][1000 genomes]
rs6843331	0.99[ASN][1000 genomes]
rs6843870	0.96[ASN][1000 genomes]
rs6844105	0.92[EUR][1000 genomes]
rs6844324	0.96[ASN][1000 genomes]
rs6846579	0.96[ASN][1000 genomes]
rs6849573	0.92[EUR][1000 genomes]
rs6853554	0.93[EUR][1000 genomes]
rs72489522	0.96[ASN][1000 genomes]
rs72677306	0.96[ASN][1000 genomes]
rs72893620	0.91[ASN][1000 genomes]
rs7340989	0.89[ASN][1000 genomes]
rs7655054	0.96[ASN][1000 genomes]
rs7657962	0.99[ASN][1000 genomes]
rs7657975	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7658011	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7658701	0.96[ASN][1000 genomes]
rs7661499	0.91[ASN][1000 genomes]
rs7661565	0.96[ASN][1000 genomes]
rs7662219	0.91[ASN][1000 genomes]
rs7662291	0.91[ASN][1000 genomes]
rs7662395	0.91[ASN][1000 genomes]
rs7662592	0.96[ASN][1000 genomes]
rs7662806	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7662836	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7664032	0.96[ASN][1000 genomes]
rs7664188	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7665946	0.91[ASN][1000 genomes]
rs7667719	0.91[ASN][1000 genomes]
rs7668477	0.91[ASN][1000 genomes]
rs7669087	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7669212	0.91[ASN][1000 genomes]
rs7671145	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7674381	0.85[ASN][1000 genomes]
rs7674466	0.90[ASN][1000 genomes]
rs7674931	0.91[ASN][1000 genomes]
rs7675728	1.00[ASN][1000 genomes]
rs7677248	0.97[ASN][1000 genomes]
rs7678229	0.96[ASN][1000 genomes]
rs7678847	0.95[ASN][1000 genomes]
rs7681257	0.96[ASN][1000 genomes]
rs7688411	0.91[ASN][1000 genomes]
rs7692069	0.94[ASN][1000 genomes]
rs7698386	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7699768	0.96[ASN][1000 genomes]
rs9684658	0.91[ASN][1000 genomes]
rs9685018	0.94[ASN][1000 genomes]
rs9685464	0.96[ASN][1000 genomes]
rs9991091	0.94[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12639678	SCYE1	Cis_1M	lymphoblastoid	RTeQTL
rs12639678	MGC16169	cis	multi-tissue	Pritchard
rs12639678	MGC16169	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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