Variant report

Variant	rs6542754
Chromosome Location	chr2:99025400-99025401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 147 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:145)

rs_ID	r²[population]
rs10199199	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10496327	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10514774	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11884553	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11888595	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11896729	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11901568	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11902825	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12052639	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12617721	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12618524	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12619665	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12622341	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13402379	0.81[AMR][1000 genomes]
rs1516085	0.82[AMR][1000 genomes]
rs1587835	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17031139	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17031146	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17031905	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17032120	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17032866	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17032870	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17033136	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17034171	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17034241	0.81[EUR][1000 genomes]
rs17444095	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17446058	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17502889	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17504774	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17505088	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17505326	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17513468	0.82[AMR][1000 genomes]
rs1847550	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2278206	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2278207	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2278208	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2278211	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2278212	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2278213	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2278214	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2309390	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3729568	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3754871	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3754872	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3754878	0.82[EUR][1000 genomes]
rs3754879	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3754880	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3754881	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3754883	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3754884	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3754885	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3754886	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3754888	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3754889	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3754890	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3754891	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3754892	0.83[ASN][1000 genomes]
rs3754893	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3769698	0.81[AMR][1000 genomes]
rs3769701	0.82[AMR][1000 genomes]
rs3769708	0.82[AMR][1000 genomes]
rs3769712	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3769713	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3769715	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3769716	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3769717	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3769719	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3769723	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3769724	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3769725	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3769726	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3769727	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3769728	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3769729	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3769730	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3769733	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3769734	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3769735	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3769736	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3769737	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3769738	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3769740	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3769741	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3769743	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3820943	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3820945	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4596026	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4599165	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4850874	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4850875	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4850876	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4850877	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4850878	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4850879	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4851131	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4851136	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4851140	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4851141	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4851142	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4851145	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4851146	0.82[AMR][1000 genomes]
rs55900716	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55934321	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56091613	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56118505	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56141907	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56197140	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56232707	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56240302	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56333112	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56357378	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58778964	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61180742	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6728891	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6736755	0.81[EUR][1000 genomes]
rs6753380	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6753515	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72819965	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72819970	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72819971	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72819972	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72819981	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72819996	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72820002	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72821904	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72821907	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72821908	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72821920	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72821924	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72821930	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72821939	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72821943	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72821946	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72821951	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72821955	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72821956	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72823792	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72823794	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72823796	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7562232	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7585747	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7585939	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7588254	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7593615	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs961242	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[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	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1006328	chr2:98977192-99210376	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6542754	UNC50	cis	Esophagus Mucosa	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99021800-99030800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:99024600-99025400	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr2:99024600-99025400	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr2:99024600-99025600	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr2:99024800-99025600	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr2:99024800-99025600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
7	chr2:99024800-99025600	Enhancers	H9 Cell Line	embryonic stem cell
8	chr2:99025000-99025600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:99025000-99025800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:99025200-99029400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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