Variant report

Variant	rs10477863
Chromosome Location	chr5:105541128-105541129
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EFNA5-3	chr5:105540921-105541178	XLOC_004950

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10037741	0.87[ASN][1000 genomes]
rs10053772	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10054814	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10057027	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10059955	0.87[ASN][1000 genomes]
rs10067178	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10477862	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10477864	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11242575	0.89[ASN][1000 genomes]
rs12513939	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12521315	0.87[ASN][1000 genomes]
rs12655359	0.84[ASN][1000 genomes]
rs12658064	0.81[ASN][1000 genomes]
rs12719552	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13167678	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13180375	0.89[ASN][1000 genomes]
rs1347404	0.80[ASN][1000 genomes]
rs1369344	0.87[ASN][1000 genomes]
rs1369345	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1435194	0.81[ASN][1000 genomes]
rs1435199	0.89[ASN][1000 genomes]
rs1435200	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1865508	0.83[ASN][1000 genomes]
rs1897942	0.81[ASN][1000 genomes]
rs1897943	0.89[ASN][1000 genomes]
rs2043502	0.89[ASN][1000 genomes]
rs2082766	0.89[ASN][1000 genomes]
rs35726927	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4260640	0.87[ASN][1000 genomes]
rs4260641	0.87[ASN][1000 genomes]
rs4457046	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4616869	0.92[ASN][1000 genomes]
rs4629569	0.89[ASN][1000 genomes]
rs4957922	0.81[ASN][1000 genomes]
rs57358218	0.82[ASN][1000 genomes]
rs62377601	0.89[ASN][1000 genomes]
rs6859823	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7712613	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7721471	0.89[ASN][1000 genomes]
rs7725559	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7731914	0.89[ASN][1000 genomes]
rs7732235	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7734007	0.88[ASN][1000 genomes]
rs7734465	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9285954	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882655	chr5:105308346-105663646	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv599285	chr5:105355890-106271223	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv882660	chr5:105358229-105685009	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv882666	chr5:105377638-105604520	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv599290	chr5:105398475-105568943	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv882668	chr5:105409644-105568943	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	esv2756534	chr5:105427073-105772632	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1028686	chr5:105458958-105624987	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv428123	chr5:105475935-106025350	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv3427509	chr5:105505316-105871362	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv462373	chr5:105507543-105795975	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv599291	chr5:105507543-105795975	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv471036	chr5:105507543-105955784	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:105540600-105543000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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