Variant report

Variant	rs558472
Chromosome Location	chr11:63149270-63149271
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:63143315..63147514-chr11:63148756..63151985,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HRASLS5-3	chr11:63148132-63151901	ucscGeneNc_uc001nxj_1

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10750998	0.99[ASN][1000 genomes]
rs1152244	0.81[EUR][1000 genomes]
rs1152245	0.83[EUR][1000 genomes]
rs1152246	0.83[EUR][1000 genomes]
rs11605137	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1193786	0.83[ASN][1000 genomes]
rs1193787	0.87[ASN][1000 genomes]
rs1193905	0.83[EUR][1000 genomes]
rs12283500	0.93[ASN][1000 genomes]
rs12293171	0.87[ASN][1000 genomes]
rs1790226	0.87[ASN][1000 genomes]
rs2958546	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3937020	0.81[EUR][1000 genomes]
rs4121881	0.94[ASN][1000 genomes]
rs471044	0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs474096	0.81[EUR][1000 genomes]
rs474191	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs474815	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs474874	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs486460	0.81[EUR][1000 genomes]
rs488803	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs494608	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4963405	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs499003	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs502642	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs505653	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs510547	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs511480	0.99[ASN][1000 genomes]
rs515213	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs516536	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs517655	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs524724	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs526686	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs527027	0.83[EUR][1000 genomes]
rs527869	0.81[EUR][1000 genomes]
rs532085	0.81[EUR][1000 genomes]
rs534799	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs538309	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs540141	0.81[EUR][1000 genomes]
rs548885	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs549144	0.80[EUR][1000 genomes]
rs556730	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs557658	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs563948	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs564917	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs565787	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs566456	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs688999	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[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	nsv1051171	chr11:62987064-63835715	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv1053585	chr11:63057767-63180308	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv555178	chr11:63078742-63197930	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv1822068	chr11:63146055-63239984	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs558472	SLC22A25	cis	Esophagus Mucosa	GTEx
rs558472	SLC22A10	cis	Esophagus Muscularis	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63141400-63153200	Weak transcription	HepG2	liver
2	chr11:63148600-63152200	Strong transcription	Liver	Liver

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