Variant report

Variant	rs439017
Chromosome Location	chr6:145806123-145806124
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 122 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs110289	0.84[EUR][1000 genomes]
rs12663211	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1292335	0.87[EUR][1000 genomes]
rs1355146	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1396648	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1883406	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1883407	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1935617	0.89[EUR][1000 genomes]
rs365515	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs365658	0.89[EUR][1000 genomes]
rs366621	0.84[EUR][1000 genomes]
rs367612	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs368848	0.85[EUR][1000 genomes]
rs369214	0.85[EUR][1000 genomes]
rs372378	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs373313	0.85[EUR][1000 genomes]
rs373321	0.85[EUR][1000 genomes]
rs373527	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs373704	0.92[EUR][1000 genomes]
rs373778	0.92[EUR][1000 genomes]
rs374000	0.85[EUR][1000 genomes]
rs374464	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs374728	0.85[EUR][1000 genomes]
rs375873	0.94[EUR][1000 genomes]
rs376991	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs377130	0.89[EUR][1000 genomes]
rs377143	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs379164	0.89[EUR][1000 genomes]
rs380883	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs382910	0.84[EUR][1000 genomes]
rs384453	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs384519	0.86[EUR][1000 genomes]
rs385134	0.86[EUR][1000 genomes]
rs386344	0.85[EUR][1000 genomes]
rs386678	0.92[EUR][1000 genomes]
rs387965	0.84[EUR][1000 genomes]
rs388394	0.85[EUR][1000 genomes]
rs388728	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs390252	0.85[EUR][1000 genomes]
rs391524	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs391820	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs392014	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs395948	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs396492	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs396681	0.83[EUR][1000 genomes]
rs397311	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs397418	0.89[EUR][1000 genomes]
rs399089	0.88[EUR][1000 genomes]
rs399516	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs400968	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs401888	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs404229	0.92[EUR][1000 genomes]
rs405622	0.90[EUR][1000 genomes]
rs406343	0.84[EUR][1000 genomes]
rs406799	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs407721	0.84[EUR][1000 genomes]
rs408768	0.84[EUR][1000 genomes]
rs411468	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs411641	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs413880	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs413916	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs414222	0.86[EUR][1000 genomes]
rs414646	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs415590	0.86[EUR][1000 genomes]
rs416243	0.84[EUR][1000 genomes]
rs416987	0.84[EUR][1000 genomes]
rs418662	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs419847	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs419850	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs419854	0.89[EUR][1000 genomes]
rs419991	0.84[EUR][1000 genomes]
rs421032	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs421268	0.86[EUR][1000 genomes]
rs421690	0.89[EUR][1000 genomes]
rs425731	0.89[EUR][1000 genomes]
rs428659	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs429306	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs430003	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs430248	0.84[EUR][1000 genomes]
rs430561	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs434298	0.86[EUR][1000 genomes]
rs436066	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs436212	0.86[EUR][1000 genomes]
rs4383831	0.91[EUR][1000 genomes]
rs441364	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs441477	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs441575	0.85[EUR][1000 genomes]
rs442254	0.86[EUR][1000 genomes]
rs442435	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs444564	0.93[EUR][1000 genomes]
rs446242	0.89[EUR][1000 genomes]
rs447818	0.84[EUR][1000 genomes]
rs449377	0.85[EUR][1000 genomes]
rs450076	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs450973	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs451349	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs452552	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs452770	0.86[EUR][1000 genomes]
rs453609	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs454370	0.86[EUR][1000 genomes]
rs454614	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs455109	0.92[EUR][1000 genomes]
rs4895678	0.87[EUR][1000 genomes]
rs585292	0.85[EUR][1000 genomes]
rs636894	0.84[EUR][1000 genomes]
rs640544	0.82[EUR][1000 genomes]
rs702313	0.82[EUR][1000 genomes]
rs9390326	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9390327	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9390329	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9399549	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9403706	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9403707	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9484995	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9497316	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs951143	0.88[EUR][1000 genomes]
rs973855	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs973856	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017166	chr6:145677071-145808448	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv604838	chr6:145709371-145841146	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv520619	chr6:145800915-145807907	Enhancers Active TSS Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	n/a
4	esv2763962	chr6:145802158-145817051	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs439017	EPM2A	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145805200-145806400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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