Variant report

Variant	rs399516
Chromosome Location	chr6:145810849-145810850
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EPM2A-2	chr6:145810766-145812318	NONHSAT115393

Extended variants
information (count: 160 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:158)

rs_ID	r²[population]
rs1045820	0.85[CEU][hapmap]
rs10872579	0.84[CEU][hapmap]
rs110289	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11155438	0.82[CEU][hapmap]
rs12663211	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1292333	0.85[CEU][hapmap]
rs1292334	0.85[CEU][hapmap]
rs1292335	0.89[CEU][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap]
rs1292336	0.85[CEU][hapmap]
rs1292337	0.85[CEU][hapmap]
rs1337839	0.85[CEU][hapmap]
rs1355146	0.85[EUR][1000 genomes]
rs1396648	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs1509213	0.85[EUR][1000 genomes]
rs1509214	0.85[EUR][1000 genomes]
rs1883406	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1883407	0.84[EUR][1000 genomes]
rs1912023	0.86[EUR][1000 genomes]
rs365515	0.85[EUR][1000 genomes]
rs365658	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs366621	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs367612	0.81[EUR][1000 genomes]
rs367643	0.82[ASN][1000 genomes]
rs368848	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs369214	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs372378	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs373313	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs373321	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs373527	0.84[EUR][1000 genomes]
rs374000	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs374464	0.80[EUR][1000 genomes]
rs374728	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs375873	0.91[EUR][1000 genomes]
rs376991	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs377130	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs377143	0.81[EUR][1000 genomes]
rs379164	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs380883	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs382910	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs384453	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs384519	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs385134	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs386344	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs387376	0.86[EUR][1000 genomes]
rs387965	0.81[EUR][1000 genomes]
rs388394	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs388728	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs390252	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs391524	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs391820	0.84[EUR][1000 genomes]
rs392014	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs395948	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs396492	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs396681	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs397311	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs397418	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs398408	0.85[EUR][1000 genomes]
rs399089	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs400968	0.85[EUR][1000 genomes]
rs401331	0.83[EUR][1000 genomes]
rs401561	0.82[EUR][1000 genomes]
rs401888	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs405206	0.83[EUR][1000 genomes]
rs406343	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs406799	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs407721	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs407887	0.83[EUR][1000 genomes]
rs408768	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs411468	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs411641	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs413880	0.85[EUR][1000 genomes]
rs413916	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs414222	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs414646	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs415590	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs416243	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs416987	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs418662	0.80[EUR][1000 genomes]
rs419847	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs419850	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs419854	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs419991	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs421032	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs421268	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs421690	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs425731	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs425999	0.86[EUR][1000 genomes]
rs428659	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs429306	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs430003	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs430248	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs430561	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs434298	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs436066	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs436212	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4383831	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs439017	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs441364	0.81[AMR][1000 genomes]
rs441477	0.82[ASN][1000 genomes]
rs441575	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs442254	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs442435	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs446242	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs447818	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs449377	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs450076	0.80[EUR][1000 genomes]
rs451108	0.82[EUR][1000 genomes]
rs451349	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs451699	0.83[EUR][1000 genomes]
rs452552	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs452770	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs453609	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs454370	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs454614	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4896832	0.85[CEU][hapmap]
rs4896833	0.85[CEU][hapmap]
rs585292	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs621382	0.86[EUR][1000 genomes]
rs636894	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs640544	0.84[ASN][1000 genomes]
rs6570701	0.85[CEU][hapmap]
rs6570703	0.90[CEU][hapmap]
rs6570705	0.85[CEU][hapmap]
rs6570708	0.82[CEU][hapmap];0.81[GIH][hapmap]
rs6918814	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6941429	0.82[CEU][hapmap]
rs697053	0.82[CEU][hapmap];0.81[GIH][hapmap]
rs697054	0.82[CEU][hapmap];0.81[GIH][hapmap]
rs697055	0.82[CEU][hapmap];0.81[GIH][hapmap]
rs702304	0.82[CEU][hapmap];0.81[GIH][hapmap]
rs702306	0.80[CEU][hapmap]
rs702307	0.82[CEU][hapmap]
rs702318	0.82[CEU][hapmap];0.81[GIH][hapmap]
rs702324	0.82[CEU][hapmap]
rs857875	0.85[CEU][hapmap]
rs857877	0.85[CEU][hapmap]
rs857879	0.85[CEU][hapmap]
rs857880	0.85[CEU][hapmap]
rs857881	0.81[CEU][hapmap]
rs857882	0.85[CEU][hapmap]
rs857883	0.85[CEU][hapmap]
rs9376945	0.83[EUR][1000 genomes]
rs9376955	0.81[CEU][hapmap]
rs9376956	0.85[CEU][hapmap]
rs9390326	0.85[EUR][1000 genomes]
rs9390327	0.83[EUR][1000 genomes]
rs9390329	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9390343	0.80[CEU][hapmap]
rs9399549	0.85[EUR][1000 genomes]
rs9399561	0.82[CEU][hapmap];0.81[GIH][hapmap]
rs9403706	0.85[EUR][1000 genomes]
rs9403707	0.85[EUR][1000 genomes]
rs9403737	0.85[CEU][hapmap]
rs9484995	0.84[EUR][1000 genomes]
rs9497316	0.83[EUR][1000 genomes]
rs9497380	0.85[CEU][hapmap]
rs973855	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs973856	0.81[AMR][1000 genomes];0.92[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	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
2	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs399516	ULBP3	trans	parietal	SCAN
rs399516	SHPRH	cis	parietal	SCAN
rs399516	EPM2A	cis	parietal	SCAN
rs399516	SHPRH	cis	cerebellum	SCAN
rs399516	RP11-545I5.3	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145810800-145812400	Enhancers	Stomach Mucosa	stomach

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