Variant report

Variant	rs1899721
Chromosome Location	chr10:116965037-116965038
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 185 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:181)

rs_ID	r²[population]
rs10444034	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10736240	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs10787554	0.95[EUR][1000 genomes]
rs10787555	1.00[CEU][hapmap];0.82[JPT][hapmap];0.97[EUR][1000 genomes]
rs10787557	0.88[CEU][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10787558	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10885649	0.81[EUR][1000 genomes]
rs10885651	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10885655	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10885657	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10885658	0.91[EUR][1000 genomes]
rs10885659	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10885660	0.91[EUR][1000 genomes]
rs10885662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10885664	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10885669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885671	1.00[CEU][hapmap];0.82[JPT][hapmap];0.94[EUR][1000 genomes]
rs10885672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885673	1.00[CEU][hapmap];0.80[CHB][hapmap];0.97[EUR][1000 genomes]
rs10885675	1.00[CEU][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes]
rs10885676	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10885677	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10885680	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10885681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10885682	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10885683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10885687	0.89[ASN][1000 genomes]
rs10885692	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10885696	0.96[CEU][hapmap];0.88[CHB][hapmap];0.80[JPT][hapmap]
rs10885700	0.82[ASN][1000 genomes]
rs10885702	0.83[ASN][1000 genomes]
rs10885705	0.81[ASN][1000 genomes]
rs10885706	0.85[ASN][1000 genomes]
rs11197066	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11197071	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11197072	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11197081	0.90[EUR][1000 genomes]
rs11197084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11197087	0.91[EUR][1000 genomes]
rs11197091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11197093	0.92[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs11197094	0.92[EUR][1000 genomes]
rs11197103	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11197107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11197110	1.00[CEU][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes]
rs11197115	0.87[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs11197122	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.94[EUR][1000 genomes]
rs11197126	1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11197127	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11197139	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11197149	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11197150	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11197159	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11197160	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11197162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11197163	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11197165	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs11197166	0.87[YRI][hapmap]
rs11197167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11197168	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11197172	0.83[ASN][1000 genomes]
rs11197180	0.86[ASN][1000 genomes]
rs11197203	0.83[ASN][1000 genomes]
rs11517121	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11525277	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11527959	0.83[ASN][1000 genomes]
rs1170884	0.85[ASN][1000 genomes]
rs12218100	1.00[CEU][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes]
rs12218477	0.83[EUR][1000 genomes]
rs12254019	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs12355617	0.88[EUR][1000 genomes]
rs12357053	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12358411	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12360503	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12573443	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1264748	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1264756	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1264763	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1264765	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs1264768	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264774	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs1264782	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1264783	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1264794	1.00[CEU][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes]
rs1264795	0.85[CEU][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs1264796	0.88[CEU][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs1264799	0.81[ASN][1000 genomes]
rs1264802	0.89[EUR][1000 genomes]
rs1268460	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1268916	0.84[EUR][1000 genomes]
rs1269602	0.99[EUR][1000 genomes]
rs1270442	0.81[CEU][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs1270654	0.81[ASN][1000 genomes]
rs1389647	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1389648	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs1537685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1565832	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1663157	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17092908	1.00[CEU][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17722681	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1899718	0.93[EUR][1000 genomes]
rs2050705	0.83[ASN][1000 genomes]
rs2050706	0.88[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap]
rs2152148	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2172669	0.95[CEU][hapmap];0.92[CHB][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2256046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2265930	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2420075	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2420077	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2420078	0.86[CEU][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2440313	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2453212	0.83[ASN][1000 genomes]
rs2484863	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs2485965	0.83[ASN][1000 genomes]
rs2485969	0.81[ASN][1000 genomes]
rs2485970	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2492980	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2492981	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2901047	0.85[ASN][1000 genomes]
rs2901048	0.85[ASN][1000 genomes]
rs34938864	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35120367	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35728982	0.88[EUR][1000 genomes]
rs4752724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5004584	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs581518	0.83[ASN][1000 genomes]
rs585908	0.83[ASN][1000 genomes]
rs589508	0.83[ASN][1000 genomes]
rs595299	0.83[ASN][1000 genomes]
rs595487	0.83[ASN][1000 genomes]
rs595931	0.83[ASN][1000 genomes]
rs595976	0.83[ASN][1000 genomes]
rs596404	0.83[ASN][1000 genomes]
rs596776	0.83[ASN][1000 genomes]
rs606204	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs608759	0.83[ASN][1000 genomes]
rs611389	0.83[ASN][1000 genomes]
rs611492	0.83[ASN][1000 genomes]
rs614722	0.83[ASN][1000 genomes]
rs615178	0.83[ASN][1000 genomes]
rs618602	0.83[ASN][1000 genomes]
rs61880825	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs620937	0.85[ASN][1000 genomes]
rs627118	0.83[ASN][1000 genomes]
rs627748	0.83[ASN][1000 genomes]
rs628063	0.83[ASN][1000 genomes]
rs628403	0.83[ASN][1000 genomes]
rs629968	0.83[ASN][1000 genomes]
rs630362	0.83[ASN][1000 genomes]
rs631520	0.85[ASN][1000 genomes]
rs631918	0.82[ASN][1000 genomes]
rs634553	0.85[ASN][1000 genomes]
rs641453	0.83[ASN][1000 genomes]
rs643922	0.83[ASN][1000 genomes]
rs646623	0.83[ASN][1000 genomes]
rs646783	0.83[ASN][1000 genomes]
rs655292	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs657139	0.83[ASN][1000 genomes]
rs657545	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs660317	0.82[ASN][1000 genomes]
rs660790	0.83[ASN][1000 genomes]
rs664158	0.83[ASN][1000 genomes]
rs665122	0.81[ASN][1000 genomes]
rs669221	0.85[ASN][1000 genomes]
rs671278	0.83[ASN][1000 genomes]
rs675802	0.83[ASN][1000 genomes]
rs677146	0.81[ASN][1000 genomes]
rs677212	0.83[ASN][1000 genomes]
rs677575	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs678664	0.83[ASN][1000 genomes]
rs685328	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs688218	0.83[ASN][1000 genomes]
rs688490	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs688611	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs693986	0.83[ASN][1000 genomes]
rs7474585	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7912050	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs840105	0.82[ASN][1000 genomes]
rs840106	0.82[ASN][1000 genomes]
rs923907	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs979009	0.83[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	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv831998	chr10:116847998-116969618	Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv869279	chr10:116884639-117032437	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv868940	chr10:116933802-117032437	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1899721	ATRNL1	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116964800-116966800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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